---
_id: '6031'
abstract:
- lang: eng
text: We introduce Clover, a new library for efficient computation using low-precision
data, providing mathematical routines required by fundamental methods in optimization
and sparse recovery. Our library faithfully implements variants of stochastic
quantization that guarantee convergence at low precision, and supports data formats
from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular,
we show that 4-bit can be implemented efficiently using Intel AVX despite the
lack of native support for this data format. Experimental results with dot product,
matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard
thresholding (IHT) demonstrate that the attainable speedups are in many cases
close to linear with respect to the reduction of precision due to reduced data
movement. Finally, for GD and IHT, we show examples of absolute speedup achieved
by 4-bit versus 32-bit, by iterating until a given target error is achieved.
article_number: '8598402'
article_processing_charge: No
author:
- first_name: Alen
full_name: Stojanov, Alen
last_name: Stojanov
- first_name: Tyler Michael
full_name: Smith, Tyler Michael
last_name: Smith
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Markus
full_name: Puschel, Markus
last_name: Puschel
citation:
ama: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on
x86: Trading compute for data movement. In: 2018 IEEE International Workshop
on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402'
apa: 'Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast
quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE
International Workshop on Signal Processing Systems (Vol. 2018–October). Cape
Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402'
chicago: 'Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel.
“Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018
IEEE International Workshop on Signal Processing Systems, Vol. 2018–October.
IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.'
ieee: 'A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized
arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International
Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol.
2018–October.'
ista: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic
on x86: Trading compute for data movement. 2018 IEEE International Workshop on
Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October,
8598402.'
mla: 'Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute
for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems,
vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.'
short: A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International
Workshop on Signal Processing Systems, IEEE, 2018.
conference:
end_date: 2018-10-24
location: Cape Town, South Africa
name: 'SiPS: Workshop on Signal Processing Systems'
start_date: 2018-10-21
date_created: 2019-02-17T22:59:25Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2023-09-19T14:41:51Z
day: '31'
department:
- _id: DaAl
doi: 10.1109/SiPS.2018.8598402
external_id:
isi:
- '000465106800060'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
publication: 2018 IEEE International Workshop on Signal Processing Systems
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fast quantized arithmetic on x86: Trading compute for data movement'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-October
year: '2018'
...
---
_id: '6032'
abstract:
- lang: eng
text: The main result of this article is a generalization of the classical blossom
algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean
CSPs where each variable appears in exactly two constraints (we call it edge CSP)
and all constraints are even Δ-matroid relations (represented by lists of tuples).
As a consequence of this, we settle the complexity classification of planar Boolean
CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then
extend the tractability result to larger classes of Δ-matroids that we call efficiently
coverable. It properly includes classes that were known to be tractable before,
namely, co-independent, compact, local, linear, and binary, with the following
caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation
by matrices. Since an n ×n matrix can represent exponentially many tuples, our
tractability result is not strictly stronger than the known algorithm for linear
and binary Δ-matroids.
article_number: '22'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of
planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649
apa: Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and
the complexity of planar boolean CSPs. ACM Transactions on Algorithms.
ACM. https://doi.org/10.1145/3230649
chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids
and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms.
ACM, 2018. https://doi.org/10.1145/3230649.
ieee: A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity
of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2.
ACM, 2018.
ista: Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity
of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.
mla: Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean
CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649.
short: A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).
date_created: 2019-02-17T22:59:25Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-20T11:20:26Z
day: '01'
department:
- _id: VlKo
doi: 10.1145/3230649
ec_funded: 1
external_id:
arxiv:
- '1602.03124'
isi:
- '000468036500007'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.03124
month: '12'
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: ACM Transactions on Algorithms
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '1192'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Even delta-matroids and the complexity of planar boolean CSPs
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...
---
_id: '606'
abstract:
- lang: eng
text: We establish the existence of a global solution for a new family of fluid-like
equations, which are obtained in certain regimes in as the mean-field evolution
of the supercurrent density in a (2D section of a) type-II superconductor with
pinning and with imposed electric current. We also consider general vortex-sheet
initial data, and investigate the uniqueness and regularity properties of the
solution. For some choice of parameters, the equation under investigation coincides
with the so-called lake equation from 2D shallow water fluid dynamics, and our
analysis then leads to a new existence result for rough initial data.
acknowledgement: "The work of the author is supported by F.R.S.-FNRS ( Fonds de la
Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Mitia
full_name: Duerinckx, Mitia
last_name: Duerinckx
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in
superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis.
2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004
apa: Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions
arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non
Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004
chicago: Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field
Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare
(C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.
ieee: M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions
arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non
Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.
ista: Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising
in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis.
35(5), 1267–1319.
mla: Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions
Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non
Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.
short: M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non
Linear Analysis 35 (2018) 1267–1319.
date_created: 2018-12-11T11:47:27Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:39:09Z
day: '01'
department:
- _id: JuFi
doi: 10.1016/j.anihpc.2017.11.004
external_id:
arxiv:
- '1607.00268'
isi:
- '000437975500005'
intvolume: ' 35'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00268
month: '08'
oa: 1
oa_version: Submitted Version
page: 1267-1319
publication: Annales de l'Institut Henri Poincare (C) Non Linear Analysis
publication_status: published
publisher: Elsevier
publist_id: '7199'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well-posedness for mean-field evolutions arising in superconductivity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 35
year: '2018'
...
---
_id: '607'
abstract:
- lang: eng
text: We study the Fokker-Planck equation derived in the large system limit of the
Markovian process describing the dynamics of quantitative traits. The Fokker-Planck
equation is posed on a bounded domain and its transport and diffusion coefficients
vanish on the domain's boundary. We first argue that, despite this degeneracy,
the standard no-flux boundary condition is valid. We derive the weak formulation
of the problem and prove the existence and uniqueness of its solutions by constructing
the corresponding contraction semigroup on a suitable function space. Then, we
prove that for the parameter regime with high enough mutation rate the problem
exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next,
we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt)
method for approximation of observables (moments) of the Fokker-Planck solution,
which can be interpreted as a nonlinear Galerkin approximation. The limited applicability
of the DynMaxEnt method inspires us to introduce its modified version that is
valid for the whole range of admissible parameters. Finally, we present several
numerical experiments to demonstrate the performance of both the original and
modified DynMaxEnt methods. We observe that in the parameter regimes where both
methods are valid, the modified one exhibits slightly better approximation properties
compared to the original one.
acknowledgement: "JH and PM are funded by KAUST baseline funds and grant no. 1000000193
.\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions.
\r\n\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Jan
full_name: Haskovec, Jan
last_name: Haskovec
- first_name: Peter
full_name: Markowich, Peter
last_name: Markowich
citation:
ama: 'Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation
for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015'
apa: 'Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum
entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear
Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015'
chicago: 'Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and
Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica
D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.'
ieee: 'K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy
approximation for the dynamics of quantitative traits,” Physica D: Nonlinear
Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.'
ista: 'Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy
approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
376–377, 108–120.'
mla: 'Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation
for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena,
vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.'
short: 'K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377
(2018) 108–120.'
date_created: 2018-12-11T11:47:28Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:38:34Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1016/j.physd.2017.10.015
external_id:
arxiv:
- '1704.08757'
isi:
- '000437962900012'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.08757
month: '08'
oa: 1
oa_version: Submitted Version
page: 108-120
publication: 'Physica D: Nonlinear Phenomena'
publication_status: published
publisher: Elsevier
publist_id: '7198'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well posedness and maximum entropy approximation for the dynamics of quantitative
traits
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 376-377
year: '2018'
...
---
_id: '608'
abstract:
- lang: eng
text: Synthesis is the automated construction of a system from its specification.
In real life, hardware and software systems are rarely constructed from scratch.
Rather, a system is typically constructed from a library of components. Lustig
and Vardi formalized this intuition and studied LTL synthesis from component libraries.
In real life, designers seek optimal systems. In this paper we add optimality
considerations to the setting. We distinguish between quality considerations (for
example, size - the smaller a system is, the better it is), and pricing (for example,
the payment to the company who manufactured the component). We study the problem
of designing systems with minimal quality-cost and price. A key point is that
while the quality cost is individual - the choices of a designer are independent
of choices made by other designers that use the same library, pricing gives rise
to a resource-allocation game - designers that use the same component share its
price, with the share being proportional to the number of uses (a component can
be used several times in a design). We study both closed and open settings, and
in both we solve the problem of finding an optimal design. In a setting with multiple
designers, we also study the game-theoretic problems of the induced resource-allocation
game.
article_processing_charge: No
article_type: original
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical
Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001
apa: Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with
costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001
chicago: Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with
Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.
ieee: G. Avni and O. Kupferman, “Synthesis from component libraries with costs,”
Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.
ista: Avni G, Kupferman O. 2018. Synthesis from component libraries with costs.
Theoretical Computer Science. 712, 50–72.
mla: Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.”
Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.
short: G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.
date_created: 2018-12-11T11:47:28Z
date_published: 2018-02-15T00:00:00Z
date_updated: 2023-09-19T10:00:21Z
day: '15'
department:
- _id: ToHe
doi: 10.1016/j.tcs.2017.11.001
ec_funded: 1
external_id:
isi:
- '000424959200003'
intvolume: ' 712'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529
month: '02'
oa: 1
oa_version: Published Version
page: 50 - 72
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '7197'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis from component libraries with costs
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 712
year: '2018'
...
---
_id: '61'
abstract:
- lang: eng
text: 'We prove that there is no strongly regular graph (SRG) with parameters (460;
153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques
in a SRG and some applications of Euclidean representation of SRGs. '
article_processing_charge: No
arxiv: 1
author:
- first_name: Andriy
full_name: Bondarenko, Andriy
last_name: Bondarenko
- first_name: Anton
full_name: Mellit, Anton
id: 388D3134-F248-11E8-B48F-1D18A9856A87
last_name: Mellit
- first_name: Andriy
full_name: Prymak, Andriy
last_name: Prymak
- first_name: Danylo
full_name: Radchenko, Danylo
last_name: Radchenko
- first_name: Maryna
full_name: Viazovska, Maryna
last_name: Viazovska
citation:
ama: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly
regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational
Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7'
apa: Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M.
(2018). There is no strongly regular graph with parameters (460; 153; 32; 60).
In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7
chicago: Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and
Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153;
32; 60).” In Contemporary Computational Mathematics, 131–34. Springer,
2018. https://doi.org/10.1007/978-3-319-72456-0_7.
ieee: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There
is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary
Computational Mathematics, Springer, 2018, pp. 131–134.
ista: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is
no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary
Computational Mathematics. , 131–134.'
mla: Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters
(460; 153; 32; 60).” Contemporary Computational Mathematics, Springer,
2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.
short: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary
Computational Mathematics, Springer, 2018, pp. 131–134.
date_created: 2018-12-11T11:44:25Z
date_published: 2018-05-23T00:00:00Z
date_updated: 2021-01-12T08:06:06Z
day: '23'
department:
- _id: TaHa
doi: 10.1007/978-3-319-72456-0_7
extern: '1'
external_id:
arxiv:
- '1509.06286'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.06286
month: '05'
oa: 1
oa_version: Preprint
page: 131 - 134
publication: Contemporary Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '7993'
quality_controlled: '1'
status: public
title: There is no strongly regular graph with parameters (460; 153; 32; 60)
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6109'
abstract:
- lang: eng
text: Neuropeptides are ubiquitous modulators of behavior and physiology. They are
packaged in specialized secretory organelles called dense core vesicles (DCVs)
that are released upon neural stimulation. Unlike synaptic vesicles, which can
be recycled and refilled close to release sites, DCVs must be replenished by de
novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in
a Caenorhabditis elegans sensory neuron whose tonic activity we can control using
a natural stimulus. We express fluorescently tagged neuropeptides in the neuron
and define parameters that describe their subcellular distribution. We measure
these parameters at high and low neural activity in 187 mutants defective in proteins
implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic
activity. Using unsupervised hierarchical clustering methods, we analyze these
data and identify 62 groups of genes with similar mutant phenotypes. We explore
the function of a subset of these groups. We recapitulate many previous findings,
validating our paradigm. We uncover a large battery of proteins involved in recycling
DCV membrane proteins, something hitherto poorly explored. We show that the unfolded
protein response promotes DCV production, which may contribute to intertissue
communication of stress. We also find evidence that different mechanisms of priming
and exocytosis may operate at high and low neural activity. Our work provides
a defined framework to study DCV biology at different neural activity levels.
author:
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: QueeLim
full_name: Ch’ng, QueeLim
last_name: Ch’ng
- first_name: Maëlle
full_name: Jospin, Maëlle
last_name: Jospin
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Ramiro
full_name: Lorenzo, Ramiro
last_name: Lorenzo
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection
of neuropeptide cell biology at high and low activity in a defined sensory neuron.
Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899.
doi:10.1073/pnas.1714610115
apa: Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M.
(2018). Genetic dissection of neuropeptide cell biology at high and low activity
in a defined sensory neuron. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115
chicago: Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro
Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at
High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115.
ieee: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic
dissection of neuropeptide cell biology at high and low activity in a defined
sensory neuron,” Proceedings of the National Academy of Sciences, vol.
115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.
ista: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic
dissection of neuropeptide cell biology at high and low activity in a defined
sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.
mla: Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at
High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National
Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018,
pp. E6890–99, doi:10.1073/pnas.1714610115.
short: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings
of the National Academy of Sciences 115 (2018) E6890–E6899.
date_created: 2019-03-19T12:41:33Z
date_published: 2018-07-17T00:00:00Z
date_updated: 2021-01-12T08:06:09Z
day: '17'
ddc:
- '570'
doi: 10.1073/pnas.1714610115
extern: '1'
external_id:
pmid:
- '29959203'
file:
- access_level: open_access
checksum: 5e81665377441cdd8d99ab952c534319
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:01:58Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6110'
file_name: 2018_PNAS_Laurent.pdf
file_size: 1567765
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E6890-E6899
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Genetic dissection of neuropeptide cell biology at high and low activity in
a defined sensory neuron
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '6111'
abstract:
- lang: eng
text: 'Neurons develop elaborate morphologies that provide a model for understanding
cellular architecture. By studying C. elegans sensory dendrites, we previously
identified genes that act to promote the extension of ciliated sensory dendrites
during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing
neuron URX is not affected by these genes, suggesting it develops through a distinct
mechanism. Here, we use a visual forward genetic screen to identify mutants that
affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15
or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before:
dendrites extend normally during embryogenesis but begin to overgrow as the animals
reach adulthood, ultimately extending up to 150% of their normal length. SMA-1
is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed
in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts
at the time of overgrowth, localizes at the dendrite ending, and requires its
kinase activity, suggesting it acts locally in time and space to constrain dendrite
growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which
normally localizes at the dendrite ending, is localized throughout the overgrown
region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically
mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond
to expansion of a sensory compartment at the dendrite ending, reminiscent of the
remodeling of sensory cilia or dendritic spines. Thus, in contrast to established
pathways that promote dendrite growth during early development, our results reveal
a distinct mechanism that constrains dendrite growth throughout the life of the
animal, possibly by controlling the size of a sensory compartment at the dendrite
ending.'
article_number: e1007435
author:
- first_name: Ian G.
full_name: McLachlan, Ian G.
last_name: McLachlan
- first_name: Isabel
full_name: Beets, Isabel
last_name: Beets
- 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: Maxwell G.
full_name: Heiman, Maxwell G.
last_name: Heiman
citation:
ama: McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains
growth of a Caenorhabditis elegans sensory dendrite throughout the life of the
organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435
apa: McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal
MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout
the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435
chicago: McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman.
“A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite
throughout the Life of the Organism.” PLOS Genetics. Public Library of
Science, 2018. https://doi.org/10.1371/journal.pgen.1007435.
ieee: I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase
constrains growth of a Caenorhabditis elegans sensory dendrite throughout the
life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of
Science, 2018.
ista: McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains
growth of a Caenorhabditis elegans sensory dendrite throughout the life of the
organism. PLOS Genetics. 14(6), e1007435.
mla: McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis
Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics,
vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435.
short: I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018).
date_created: 2019-03-19T13:09:28Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '07'
ddc:
- '570'
doi: 10.1371/journal.pgen.1007435
extern: '1'
external_id:
pmid:
- '29879119'
file:
- access_level: open_access
checksum: 622036b945365dbc575bea2768aa9bc8
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:18:01Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6112'
file_name: 2018_PLOS_McLachlan.pdf
file_size: 13011506
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory
dendrite throughout the life of the organism
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2018'
...
---
_id: '612'
abstract:
- lang: eng
text: Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically
and postsynaptically through the modulation of different effector signalling pathways.
Here, we analysed the distribution of GABAB receptors using highly sensitive SDS-digested
freeze-fracture replica labelling in mouse cerebellar Purkinje cells. Immunoreactivity
for GABAB1 was observed on presynaptic and, more abundantly, on postsynaptic compartments,
showing both scattered and clustered distribution patterns. Quantitative analysis
of immunoparticles revealed a somato-dendritic gradient, with the density of immunoparticles
increasing 26-fold from somata to dendritic spines. To understand the spatial
relationship of GABAB receptors with two key effector ion channels, the G protein-gated
inwardly rectifying K+ (GIRK/Kir3) channel and the voltage-dependent Ca2+ channel,
biochemical and immunohistochemical approaches were performed. Co-immunoprecipitation
analysis demonstrated that GABAB receptors co-assembled with GIRK and CaV2.1 channels
in the cerebellum. Using double-labelling immunoelectron microscopic techniques,
co-clustering between GABAB1 and GIRK2 was detected in dendritic spines, whereas
they were mainly segregated in the dendritic shafts. In contrast, co-clustering
of GABAB1 and CaV2.1 was detected in dendritic shafts but not spines. Presynaptically,
although no significant co-clustering of GABAB1 and GIRK2 or CaV2.1 channels was
detected, inter-cluster distance for GABAB1 and GIRK2 was significantly smaller
in the active zone than in the dendritic shafts, and that for GABAB1 and CaV2.1
was significantly smaller in the active zone than in the dendritic shafts and
spines. Thus, GABAB receptors are associated with GIRK and CaV2.1 channels in
different subcellular compartments. These data provide a better framework for
understanding the different roles played by GABAB receptors and their effector
ion channels in the cerebellar network.
article_processing_charge: No
article_type: original
author:
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Carolina
full_name: Aguado, Carolina
last_name: Aguado
- first_name: Francisco
full_name: Ciruela, Francisco
last_name: Ciruela
- first_name: Javier
full_name: Cózar, Javier
last_name: Cózar
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Luis
full_name: De La Ossa, Luis
last_name: De La Ossa
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Kevin
full_name: Wickman, Kevin
last_name: Wickman
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
citation:
ama: Luján R, Aguado C, Ciruela F, et al. Differential association of GABAB receptors
with their effector ion channels in Purkinje cells. Brain Structure and Function.
2018;223(3):1565-1587. doi:10.1007/s00429-017-1568-y
apa: Luján, R., Aguado, C., Ciruela, F., Cózar, J., Kleindienst, D., De La Ossa,
L., … Fukazawa, Y. (2018). Differential association of GABAB receptors with their
effector ion channels in Purkinje cells. Brain Structure and Function.
Springer. https://doi.org/10.1007/s00429-017-1568-y
chicago: Luján, Rafael, Carolina Aguado, Francisco Ciruela, Javier Cózar, David
Kleindienst, Luis De La Ossa, Bernhard Bettler, et al. “Differential Association
of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain
Structure and Function. Springer, 2018. https://doi.org/10.1007/s00429-017-1568-y.
ieee: R. Luján et al., “Differential association of GABAB receptors with
their effector ion channels in Purkinje cells,” Brain Structure and Function,
vol. 223, no. 3. Springer, pp. 1565–1587, 2018.
ista: Luján R, Aguado C, Ciruela F, Cózar J, Kleindienst D, De La Ossa L, Bettler
B, Wickman K, Watanabe M, Shigemoto R, Fukazawa Y. 2018. Differential association
of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure
and Function. 223(3), 1565–1587.
mla: Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their
Effector Ion Channels in Purkinje Cells.” Brain Structure and Function,
vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y.
short: R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa,
B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure
and Function 223 (2018) 1565–1587.
date_created: 2018-12-11T11:47:29Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2024-03-25T23:30:16Z
day: '01'
ddc:
- '571'
department:
- _id: RySh
doi: 10.1007/s00429-017-1568-y
ec_funded: 1
external_id:
isi:
- '000428419500030'
file:
- access_level: open_access
checksum: a55b3103476ecb5f4f983d8801807e8b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:36Z
date_updated: 2020-07-14T12:47:20Z
file_id: '5157'
file_name: IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf
file_size: 5542926
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 223'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1565 - 1587
project:
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Brain Structure and Function
publication_status: published
publisher: Springer
publist_id: '7192'
pubrep_id: '1013'
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Differential association of GABAB receptors with their effector ion channels
in Purkinje cells
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: 223
year: '2018'
...
---
_id: '616'
abstract:
- lang: eng
text: Social insects protect their colonies from infectious disease through collective
defences that result in social immunity. In ants, workers first try to prevent
infection of colony members. Here, we show that if this fails and a pathogen establishes
an infection, ants employ an efficient multicomponent behaviour − "destructive
disinfection" − to prevent further spread of disease through the colony.
Ants specifically target infected pupae during the pathogen's non-contagious incubation
period, relying on chemical 'sickness cues' emitted by pupae. They then remove
the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which
enters the body and prevents pathogen replication from the inside out. Like the
immune system of a body that specifically targets and eliminates infected cells,
this social immunity measure sacrifices infected brood to stop the pathogen completing
its lifecycle, thus protecting the rest of the colony. Hence, the same principles
of disease defence apply at different levels of biological organisation.
article_number: e32073
article_processing_charge: Yes
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected
brood prevents systemic disease spread in ant colonies. eLife. 2018;7.
doi:10.7554/eLife.32073
apa: Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt,
T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic
disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073
chicago: Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse,
Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection
of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife.
eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.
ieee: C. Pull et al., “Destructive disinfection of infected brood prevents
systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences
Publications, 2018.
ista: Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown
M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic
disease spread in ant colonies. eLife. 7, e32073.
mla: Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents
Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife
Sciences Publications, 2018, doi:10.7554/eLife.32073.
short: C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt,
M. Brown, S. Cremer, ELife 7 (2018).
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-09T00:00:00Z
date_updated: 2023-09-11T12:54:26Z
day: '09'
ddc:
- '570'
- '590'
department:
- _id: SyCr
doi: 10.7554/eLife.32073
ec_funded: 1
external_id:
isi:
- '000419601300001'
file:
- access_level: open_access
checksum: 540f941e8d3530a9441e4affd94f07d7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:43Z
date_updated: 2020-07-14T12:47:20Z
file_id: '4832'
file_name: IST-2018-978-v1+1_elife-32073-v1.pdf
file_size: 1435585
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DDF0F0-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '302004'
name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities
in ant societies: a chemo-neuro-immunological approach'
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7188'
pubrep_id: '978'
quality_controlled: '1'
related_material:
record:
- id: '819'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Destructive disinfection of infected brood prevents systemic disease spread
in ant colonies
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: 7
year: '2018'
...
---
_id: '6164'
abstract:
- lang: eng
text: In this paper, we propose an algorithm to build discrete spherical shell having
integer center and real-valued inner and outer radii on the face-centered cubic
(FCC) grid. We address the problem by mapping it to a 2D scenario and building
the shell layer by layer on hexagonal grids with additive manufacturing in mind.
The layered hexagonal grids get shifted according to need as we move from one
layer to another and forms the FCC grid in 3D. However, we restrict our computation
strictly to 2D in order to utilize symmetry and simplicity.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Girish
full_name: Koshti, Girish
last_name: Koshti
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Gaëlle
full_name: Largeteau-Skapin, Gaëlle
last_name: Largeteau-Skapin
- first_name: Rita
full_name: Zrour, Rita
last_name: Zrour
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere
construction on the FCC grid interpreted as layered hexagonal grids in 3D. In:
19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7'
apa: 'Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., &
Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered
hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp.
82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7'
chicago: 'Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric
Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted
as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96.
Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.'
ieee: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick,
“Sphere construction on the FCC grid interpreted as layered hexagonal grids in
3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255,
pp. 82–96.
ista: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018.
Sphere construction on the FCC grid interpreted as layered hexagonal grids in
3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial
Image Analysis, LNCS, vol. 11255, 82–96.'
mla: Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as
Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255,
Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7.
short: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick,
in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96.
conference:
end_date: 2018-11-24
location: Porto, Portugal
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2018-11-22
date_created: 2019-03-21T12:16:58Z
date_published: 2018-11-22T00:00:00Z
date_updated: 2022-01-27T15:26:39Z
day: '22'
doi: 10.1007/978-3-030-05288-1_7
extern: '1'
intvolume: ' 11255'
language:
- iso: eng
month: '11'
oa_version: None
page: 82-96
place: Cham
publication: 19th International Workshop
publication_identifier:
eisbn:
- 978-3-030-05288-1
eissn:
- 1611-3349
isbn:
- 978-3-030-05287-4
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: Sphere construction on the FCC grid interpreted as layered hexagonal grids
in 3D
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11255
year: '2018'
...
---
_id: '617'
abstract:
- lang: eng
text: Insects are exposed to a variety of potential pathogens in their environment,
many of which can severely impact fitness and health. Consequently, hosts have
evolved resistance and tolerance strategies to suppress or cope with infections.
Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads,
and hosts utilizing tolerance reduce harmful fitness effects per pathogen load.
To understand variation in, and selective pressures on, resistance and tolerance,
we asked to what degree they are shaped by host genetic background, whether plasticity
in these responses depends upon dietary environment, and whether there are interactions
between these two factors. Females from ten wild-type Drosophila melanogaster
genotypes were kept on high- or low-protein (yeast) diets and infected with one
of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila.
We measured host resistance as the inverse of bacterial load in the early infection
phase. The relationship (slope) between fly fecundity and individual-level bacteria
load provided our fecundity tolerance measure. Genotype and dietary yeast determined
host fecundity and strongly affected survival after infection with pathogenic
P. entomophila. There was considerable genetic variation in host resistance, a
commonly found phenomenon resulting from for example varying resistance costs
or frequency-dependent selection. Despite this variation and the reproductive
cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes.
The absence of genetic variation in tolerance may suggest that at this early infection
stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are
not expressed under these infection conditions.
acknowledgement: 'We would like to thank Susann Wicke for performing the genome-wide
SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara
Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical
help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the
Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for
their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG)
priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR
872/1-1). '
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival,
and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
2018;31(1):159-171. doi:10.1111/jeb.13211
apa: Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect
resistance, survival, and fecundity but not fecundity tolerance. Journal of
Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect
Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of
Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.
ieee: M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary
Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.
ista: Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
31(1), 159–171.
mla: Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity
but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31,
no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.
short: M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018)
159–171.
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T14:06:04Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/jeb.13211
external_id:
isi:
- '000419307000014'
pmid:
- '29150962'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13211
month: '01'
oa: 1
oa_version: Published Version
page: 159 - 171
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '7187'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genotype and diet affect resistance, survival, and fecundity but not fecundity
tolerance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 31
year: '2018'
...
---
_id: '6183'
abstract:
- lang: eng
text: "We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z
- a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq
0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element
of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$.
We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued
measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this
measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect
to the Lebesgue measure, which\r\nis supported on finitely many intervals, called
bands. In fact, the density is\r\nanalytic inside the bands with a square-root
growth at the edges and internal\r\ncubic root cusps whenever the gap between
two bands vanishes. The shape of\r\nthese singularities is universal and no other
singularity may occur. We give a\r\nprecise asymptotic description of $m$ near
the singular points. These\r\nasymptotics generalize the analysis at the regular
edges given in the companion\r\npaper on the Tracy-Widom universality for the
edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744]
and they play a key role in the\r\nproof of the Pearcey universality at the cusp
for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend
the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von
Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically
rigid under\r\ndeformations and we conclude that these masses are quantized in
some important\r\ncases."
article_number: '1804.07752'
article_processing_charge: No
arxiv: 1
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: 'Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral
bands, edges and cusps. arXiv.'
apa: 'Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear
self-energy: Spectral bands, edges and cusps. arXiv.'
chicago: 'Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation
with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.'
ieee: 'J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy:
Spectral bands, edges and cusps,” arXiv. .'
ista: 'Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral
bands, edges and cusps. arXiv, 1804.07752.'
mla: 'Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral
Bands, Edges and Cusps.” ArXiv, 1804.07752.'
short: J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).
date_created: 2019-03-28T09:20:06Z
date_published: 2018-04-20T00:00:00Z
date_updated: 2023-12-18T10:46:08Z
day: '20'
department:
- _id: LaEr
external_id:
arxiv:
- '1804.07752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.07752
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
- id: '14694'
relation: later_version
status: public
status: public
title: 'The Dyson equation with linear self-energy: Spectral bands, edges and cusps'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6195'
abstract:
- lang: eng
text: In the context of robotic manipulation and grasping, the shift from a view
that is static (force closure of a single posture) and contact-deprived (only
contact for force closure is allowed, everything else is obstacle) towards a view
that is dynamic and contact-rich (soft manipulation) has led to an increased interest
in soft hands. These hands can easily exploit environmental constraints and object
surfaces without risk, and safely interact with humans, but present also some
challenges. Designing them is difficult, as well as predicting, modelling, and
“programming” their interactions with the objects and the environment. This paper
tackles the problem of simulating them in a fast and effective way, leveraging
on novel and existing simulation technologies. We present a triple-layered simulation
framework where dynamic properties such as stiffness are determined from slow
but accurate FEM simulation data once, and then condensed into a lumped parameter
model that can be used to fast simulate soft fingers and soft hands. We apply
our approach to the simulation of soft pneumatic fingers.
article_number: '8461106'
article_processing_charge: No
author:
- first_name: Maria
full_name: Pozzi, Maria
last_name: Pozzi
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
orcid: 0000-0001-5665-0430
- first_name: Raphael
full_name: Deimel, Raphael
last_name: Deimel
- first_name: Monica
full_name: Malvezzi, Monica
last_name: Malvezzi
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Oliver
full_name: Brock, Oliver
last_name: Brock
- first_name: Domenico
full_name: Prattichizzo, Domenico
last_name: Prattichizzo
citation:
ama: 'Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation
of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106'
apa: 'Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock,
O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots
modeled as kinematic chains. Presented at the ICRA: International Conference on
Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106'
chicago: Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd
Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation
of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.
ieee: 'M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled
as kinematic chains,” presented at the ICRA: International Conference on Robotics
and Automation, Brisbane, Australia, 2018.'
ista: 'Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo
D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains.
ICRA: International Conference on Robotics and Automation, 8461106.'
mla: Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled
as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106.
short: M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock,
D. Prattichizzo, in:, IEEE, 2018.
conference:
end_date: 2018-05-25
location: Brisbane, Australia
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2018-05-21
date_created: 2019-04-04T09:50:38Z
date_published: 2018-09-10T00:00:00Z
date_updated: 2023-09-19T14:49:03Z
day: '10'
department:
- _id: BeBi
doi: 10.1109/icra.2018.8461106
external_id:
isi:
- '000446394503031'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
publication_identifier:
isbn:
- '9781538630815'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient FEM-based simulation of soft robots modeled as kinematic chains
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '62'
abstract:
- lang: eng
text: Imaging is a dominant strategy for data collection in neuroscience, yielding
stacks of images that often scale to gigabytes of data for a single experiment.
Machine learning algorithms from computer vision can serve as a pair of virtual
eyes that tirelessly processes these images, automatically detecting and identifying
microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction
of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual
clues and requires no training. This approach generalizes across different modalities,
including serially-sectioned scanning electron microscopy (sSEM) of genetically
labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe)
microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue
volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets,
demonstrating the high biological fidelity of the pipeline’s reconstructions.
FLoRIN reconstructions are of sufficient quality for preliminary biological study,
for example examining the distribution and morphology of cells or extracting single
axons from functional data. Compared to existing supervised learning methods,
FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions
that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.
acknowledgement: 'Equipment was generously donated by the NVIDIA Corporation, and
made available by the National Science Foundation (NSF) through grant #CNS-1629914.
This research used resources of the Argonne Leadership Computing Facility, which
is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.'
article_number: '14247'
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Shabazi, Ali
last_name: Shabazi
- first_name: Jeffery
full_name: Kinnison, Jeffery
last_name: Kinnison
- first_name: Rafael
full_name: Vescovi, Rafael
last_name: Vescovi
- first_name: Ming
full_name: Du, Ming
last_name: Du
- first_name: Robert
full_name: Hill, Robert
last_name: Hill
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Marc
full_name: Takeno, Marc
last_name: Takeno
- first_name: Hongkui
full_name: Zeng, Hongkui
last_name: Zeng
- first_name: Nuno
full_name: Da Costa, Nuno
last_name: Da Costa
- first_name: Jaime
full_name: Grutzendler, Jaime
last_name: Grutzendler
- first_name: Narayanan
full_name: Kasthuri, Narayanan
last_name: Kasthuri
- first_name: Walter
full_name: Scheirer, Walter
last_name: Scheirer
citation:
ama: Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation
and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3
apa: Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer,
W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3
chicago: Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian
A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018.
https://doi.org/10.1038/s41598-018-32628-3.
ieee: A. Shabazi et al., “Flexible learning-free segmentation and reconstruction
of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing
Group, 2018.
ista: Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H,
Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free
segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.
mla: Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing
Group, 2018, doi:10.1038/s41598-018-32628-3.
short: A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno,
H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports
8 (2018).
date_created: 2018-12-11T11:44:25Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2023-09-11T14:02:55Z
day: '24'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-018-32628-3
external_id:
isi:
- '000445336600015'
file:
- access_level: open_access
checksum: 1a14ae0666b82fbaa04bef110e3f6bf2
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:22:24Z
date_updated: 2020-07-14T12:47:24Z
file_id: '5699'
file_name: 2018_ScientificReports_Shahbazi.pdf
file_size: 4141645
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7992'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: http://doi.org/10.1038/s41598-018-36220-7
scopus_import: '1'
status: public
title: Flexible learning-free segmentation and reconstruction of neural volumes
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: 8
year: '2018'
...
---
_id: '620'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis requires the coordinated assembly of various
endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates
a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis,
but specific roles for PtdIns(4)P other than as the biosynthetic precursor of
PtdIns(4,5)P2 have not been clarified. In this study we investigated the role
of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction
of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and
the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that
both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic
internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts)
and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment
of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2
is required for membrane internalization. We also found that the localization
to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p
and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant,
but not in the mss4(ts) mutant. These results suggest distinct roles in successive
steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.
article_number: jcs207696
article_processing_charge: No
author:
- first_name: Wataru
full_name: Yamamoto, Wataru
last_name: Yamamoto
- first_name: Suguru
full_name: Wada, Suguru
last_name: Wada
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns
4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of
Cell Science. 2018;131(1). doi:10.1242/jcs.207696
apa: Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima,
J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and
PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.207696
chicago: Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus,
Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4
P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of
Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.
ieee: W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P
and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell
Science, vol. 131, no. 1. Company of Biologists, 2018.
ista: Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J.
2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast
receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.
mla: Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and
PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell
Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.
short: W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J.
Toshima, Journal of Cell Science 131 (2018).
date_created: 2018-12-11T11:47:32Z
date_published: 2018-01-04T00:00:00Z
date_updated: 2023-09-11T12:57:13Z
day: '04'
department:
- _id: DaSi
doi: 10.1242/jcs.207696
external_id:
isi:
- '000424786900012'
pmid:
- '29192062'
intvolume: ' 131'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29192062
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '7184'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast
receptor mediated endocytosis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 131
year: '2018'
...
---
_id: '6263'
abstract:
- lang: eng
text: 'Antibiotic resistance can emerge spontaneously through genomic mutation and render
treatment ineffective. To counteract this process, in addition to the discovery and
description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand
its determinantsis needed. To address this challenge, this thesisuncoversnew genetic
determinants of resistance evolvability using a customized robotic setup,
exploressystematic ways in which resistance evolution is perturbed due to
dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates
the evolutionary fate of one specific type of evolvability modifier -a stress-induced
mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order
to identify them, we first developedan automated high-throughput feedback-controlled
protocol whichkeeps the population size and selection pressure approximately constant
for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic
concentration. We implementedthis protocol on a customized liquid handling robot and
propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100
generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more
compared to less sensitive ones. Our data uncover that deletions of certain genes
which do not affect mutation rate,including efflux pump components, a chaperone and
severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution.
Sequencing analysis of evolved populations indicates that epistasis with resistance
mutations is the most likelyexplanation. This work could inspire treatment strategies in
which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to
slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model,
toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence
evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations.
We show that in silicothis also leads to slower resistance evolution. We
see and confirm with experiments that increased mutation rates, apart from speeding
up evolution, also leadto high reproducibility of phenotypic adaptation in a context
of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic
resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier
–a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under
periodic selectionakin to clinical treatment. We set up a deterministic
infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and
evaluate various treatment schemes in how well they maintain a stress-induced
mutator allele. In particular,a high diversity of stresses is crucial for the persistence
of the mutator allele. This leads to a general trade-off where exactly those
diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly
evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular
mechanisms involved in antibiotic resistance evolution and could inspire new strategies
for slowing down its rate. '
acknowledged_ssus:
- _id: M-Shop
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
citation:
ama: Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018.
doi:10.15479/AT:ISTA:th1072
apa: Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072
chicago: Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072.
ieee: M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,”
Institute of Science and Technology Austria, 2018.
ista: Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution.
Institute of Science and Technology Austria.
mla: Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.
short: M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution,
Institute of Science and Technology Austria, 2018.
date_created: 2019-04-09T13:57:15Z
date_published: 2018-12-28T00:00:00Z
date_updated: 2023-09-22T09:20:37Z
day: '28'
ddc:
- '570'
- '576'
- '579'
degree_awarded: PhD
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:th1072
file:
- access_level: open_access
checksum: fc60585c9eaad868ac007004ef130908
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T13:49:24Z
date_updated: 2021-02-11T11:17:17Z
embargo: 2020-01-25
file_id: '6264'
file_name: 2018_Thesis_Lukacisinova.pdf
file_size: 5656866
relation: main_file
- access_level: closed
checksum: 264057ec0a92ab348cc83b41f021ba92
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-09T13:49:23Z
date_updated: 2020-07-14T12:47:25Z
embargo_to: open_access
file_id: '6265'
file_name: 2018_Thesis_Lukacisinova_source.docx
file_size: 5168054
relation: source_file
file_date_updated: 2021-02-11T11:17:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '91'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1619'
relation: part_of_dissertation
status: public
- id: '696'
relation: part_of_dissertation
status: public
- id: '1027'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Genetic determinants of antibiotic resistance evolution
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '6266'
abstract:
- lang: eng
text: 'A major challenge in neuroscience research is to dissect the circuits that
orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian
species, such as microbial opsins, have been successfully transplanted to specific
neuronal targets to override their natural communication patterns. The goal of
our work is to manipulate synaptic communication in a manner that closely incorporates
the functional intricacies of synapses by preserving temporal encoding (i.e. the
firing pattern of the presynaptic neuron) and connectivity (i.e. target specific
synapses rather than specific neurons). Our strategy to achieve this goal builds
on the use of non-mammalian transplants to create a synthetic synapse. The mode
of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN)
into synaptic vesicles by means of a genetically targeted transporter selective
for the SN. Upon natural vesicular release, exposure of the SN to the synaptic
cleft will modify the post-synaptic potential through an orthogonal ligand gated
ion channel. To achieve this goal we have functionally characterized a mixed cationic
methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally
characterize a synthetic transporter in isolated synaptic vesicles without the
need for transgenic animals, identified and extracted multiple prokaryotic uptake
systems that are substrate specific for methionine (Met), and established a primary/cell
line co-culture system that would allow future combinatorial testing of this orthogonal
transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique
opportunity to manipulate synaptic communication while maintaining the electrophysiological
integrity of the pre-synaptic cell. In this way, information may be preserved
that was generated in upstream circuits and that could be essential for concerted
function and information processing. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
citation:
ama: Mckenzie C. Design and characterization of methods and biological components
to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055
apa: Mckenzie, C. (2018). Design and characterization of methods and biological
components to realize synthetic neurotransmission . Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:th_1055
chicago: Mckenzie, Catherine. “Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission .” Institute of Science and
Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.
ieee: C. Mckenzie, “Design and characterization of methods and biological components
to realize synthetic neurotransmission ,” Institute of Science and Technology
Austria, 2018.
ista: Mckenzie C. 2018. Design and characterization of methods and biological components
to realize synthetic neurotransmission . Institute of Science and Technology Austria.
mla: Mckenzie, Catherine. Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission . Institute of Science and
Technology Austria, 2018, doi:10.15479/at:ista:th_1055.
short: C. Mckenzie, Design and Characterization of Methods and Biological Components
to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria,
2018.
date_created: 2019-04-09T14:13:39Z
date_published: 2018-10-31T00:00:00Z
date_updated: 2023-09-07T13:02:37Z
day: '31'
ddc:
- '571'
- '573'
degree_awarded: PhD
department:
- _id: HaJa
doi: 10.15479/at:ista:th_1055
file:
- access_level: open_access
checksum: 9d2c2dca04b00e485470c28b262af59a
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T14:12:40Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2019-11-24
file_id: '6267'
file_name: 2018_Thesis_McKenzie.pdf
file_size: 4906420
relation: main_file
- access_level: closed
checksum: 50b58c272899601bc6fd9642c4dc97f1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-09T14:12:40Z
date_updated: 2020-07-14T12:47:25Z
embargo_to: open_access
file_id: '6268'
file_name: 2018_Thesis_McKenzie_source.docx
file_size: 5053545
relation: source_file
file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '95'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
pubrep_id: '1055'
related_material:
record:
- id: '7132'
relation: new_edition
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: 'Design and characterization of methods and biological components to realize
synthetic neurotransmission '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '63'
abstract:
- lang: eng
text: African cichlids display a remarkable assortment of jaw morphologies, pigmentation
patterns, and mating behaviors. In addition to this previously documented diversity,
recent studies have documented a rich diversity of sex chromosomes within these
fishes. Here we review the known sex-determination network within vertebrates,
and the extraordinary number of sex chromosomes systems segregating in African
cichlids. We also propose a model for understanding the unusual number of sex
chromosome systems within this clade.
acknowledgement: NSF DEB-1830753 and ISTPlus Fellowship
article_number: '480'
article_processing_charge: No
author:
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Thomas
full_name: Kocher, Thomas
last_name: Kocher
citation:
ama: Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African
cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480
apa: Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes
in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480
chicago: Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.
ieee: W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in
African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.
ista: Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African
cichlid fishes. Genes. 9(10), 480.
mla: Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018,
doi:10.3390/genes9100480.
short: W.J. Gammerdinger, T. Kocher, Genes 9 (2018).
date_created: 2018-12-11T11:44:26Z
date_published: 2018-10-04T00:00:00Z
date_updated: 2023-09-19T10:37:03Z
day: '04'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes9100480
ec_funded: 1
external_id:
isi:
- '000448656700018'
file:
- access_level: open_access
checksum: bec527692e2c9b56919c0429634ff337
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:54:46Z
date_updated: 2020-07-14T12:47:27Z
file_id: '5743'
file_name: 2018_Genes_Gammerdinger.pdf
file_size: 1415791
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genes
publication_status: published
publisher: MDPI AG
publist_id: '7991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unusual diversity of sex chromosomes in African cichlid fishes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '6339'
abstract:
- lang: eng
text: We introduce a diagrammatic Monte Carlo approach to angular momentum properties
of quantum many-particle systems possessing a macroscopic number of degrees of
freedom. The treatment is based on a diagrammatic expansion that merges the usual
Feynman diagrams with the angular momentum diagrams known from atomic and nuclear
structure theory, thereby incorporating the non-Abelian algebra inherent to quantum
rotations. Our approach is applicable at arbitrary coupling, is free of systematic
errors and of finite-size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model; however, the method is quite general and can be applied
to a broad variety of systems in which particles exchange quantum angular momentum
with their many-body environment.
article_number: '165301'
article_processing_charge: No
arxiv: 1
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular
momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16).
doi:10.1103/physrevlett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to angular momentum in quantum many-particle systems. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo
Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review
Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems,” Physical Review Letters,
vol. 121, no. 16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems. Physical Review Letters.
121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum
in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no.
16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-04-17T10:53:38Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2024-02-28T13:15:09Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/physrevlett.121.165301
external_id:
arxiv:
- '1803.07990'
isi:
- '000447468400008'
intvolume: ' 121'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle
systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...