---
_id: '11417'
abstract:
- lang: eng
text: "Over the past few years, the field of quantum information science has seen
tremendous progress toward realizing large-scale quantum computers. With demonstrations
of quantum computers outperforming classical computers for a select range of problems,1–3
we have finally entered the noisy, intermediate-scale quantum (NISQ) computing
era. While the quantum computers of today are technological marvels, they are
not yet error corrected, and it is unclear whether any system will scale beyond
a few hundred logical qubits without significant changes to architecture and control
schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical
Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer)
systems of the 1940s, which ran on vacuum tubes. These machines were built on
a solid, nominally scalable architecture and when they were developed, nobody
could have predicted the development of the transistor and the impact of the resulting
semiconductor industry. Simply put, the computers of today are nothing like the
early computers of the 1940s. We believe that the qubits of future fault-tolerant
quantum systems will look quite different from the qubits of the NISQ machines
in operation today. This Special Topic issue is devoted to new and emerging quantum
systems with a focus on enabling technologies that can eventually lead to the
quantum analog to the transistor. We have solicited both research4–18 and perspective
articles19–21 to discuss new and emerging qubit systems with a focus on novel
materials, encodings, and architectures. We are proud to present a collection
that touches on a wide range of technologies including superconductors,7–13,21
semiconductors,15–17,19 and individual atomic qubits.18\r\n"
acknowledgement: "We would like to thank all of the authors who contributed to\r\nthis
Special Topic. We would also like to thank the editorial team at\r\nAPL including
Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen."
article_number: '190401'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anthony J.
full_name: Sigillito, Anthony J.
last_name: Sigillito
- first_name: Jacob P.
full_name: Covey, Jacob P.
last_name: Covey
- 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: Karl
full_name: Petersson, Karl
last_name: Petersson
- first_name: Stefan
full_name: Preble, Stefan
last_name: Preble
citation:
ama: 'Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems:
Guest editorial. Applied Physics Letters. 2022;120(19). doi:10.1063/5.0097339'
apa: 'Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., & Preble,
S. (2022). Emerging qubit systems: Guest editorial. Applied Physics Letters.
American Institute of Physics. https://doi.org/10.1063/5.0097339'
chicago: 'Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson,
and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” Applied Physics
Letters. American Institute of Physics, 2022. https://doi.org/10.1063/5.0097339.'
ieee: 'A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging
qubit systems: Guest editorial,” Applied Physics Letters, vol. 120, no.
19. American Institute of Physics, 2022.'
ista: 'Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit
systems: Guest editorial. Applied Physics Letters. 120(19), 190401.'
mla: 'Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” Applied
Physics Letters, vol. 120, no. 19, 190401, American Institute of Physics,
2022, doi:10.1063/5.0097339.'
short: A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics
Letters 120 (2022).
date_created: 2022-05-29T22:01:53Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2023-08-03T07:16:20Z
day: '12'
department:
- _id: JoFi
doi: 10.1063/5.0097339
external_id:
isi:
- '000796002100002'
intvolume: ' 120'
isi: 1
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/5.0097339
month: '05'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Emerging qubit systems: Guest editorial'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2022'
...
---
_id: '11418'
abstract:
- lang: eng
text: "We consider the quadratic form of a general high-rank deterministic matrix
on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian
fluctuation for each bulk eigenvector in the large N limit. The proof is a combination
of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau
(2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021)
1005–1048)."
acknowledgement: L.E. would like to thank Zhigang Bao for many illuminating discussions
in an early stage of this research. The authors are also grateful to Paul Bourgade
for his comments on the manuscript and the anonymous referee for several useful
suggestions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity
for Wigner matrices. Annals of Probability. 2022;50(3):984-1012. doi:10.1214/21-AOP1552
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Normal fluctuation
in quantum ergodicity for Wigner matrices. Annals of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/21-AOP1552
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation
in Quantum Ergodicity for Wigner Matrices.” Annals of Probability. Institute
of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AOP1552.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum
ergodicity for Wigner matrices,” Annals of Probability, vol. 50, no. 3.
Institute of Mathematical Statistics, pp. 984–1012, 2022.
ista: Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity
for Wigner matrices. Annals of Probability. 50(3), 984–1012.
mla: Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner
Matrices.” Annals of Probability, vol. 50, no. 3, Institute of Mathematical
Statistics, 2022, pp. 984–1012, doi:10.1214/21-AOP1552.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.
date_created: 2022-05-29T22:01:53Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-03T07:16:53Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/21-AOP1552
external_id:
arxiv:
- '2103.06730'
isi:
- '000793963400005'
intvolume: ' 50'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.06730
month: '05'
oa: 1
oa_version: Preprint
page: 984-1012
publication: Annals of Probability
publication_identifier:
eissn:
- 2168-894X
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Normal fluctuation in quantum ergodicity for Wigner matrices
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 50
year: '2022'
...
---
_id: '11419'
abstract:
- lang: eng
text: Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in
Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission
at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human
tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly
and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements
revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking
MT assembly using nocodazole prevented tau-induced impairments of endocytosis
and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly
by WT h-tau loading was associated with an increased MT-bound fraction of the
endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin
1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced
impairments of endocytosis and neurotransmission. We conclude that elevation of
presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free
dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired,
causing activity-dependent rundown of neurotransmission.
acknowledgement: We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments
and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako
Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda
for technical assistant with in vitro analysis of tau. This research was supported
by funding from Okinawa Institute of Science and Technology and from Technology
(OIST) and Core Research for the Evolutional Science and Technology of Japan Science
and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas
to TM (Brain Protein Aging and Dementia Control 26117004).
article_number: e73542
article_processing_charge: No
article_type: original
author:
- first_name: Tetsuya
full_name: Hori, Tetsuya
last_name: Hori
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Han Ying
full_name: Wang, Han Ying
last_name: Wang
- first_name: Tomohiro
full_name: Miyasaka, Tomohiro
last_name: Miyasaka
- first_name: Laurent
full_name: Guillaud, Laurent
last_name: Guillaud
- first_name: Zacharie
full_name: Taoufiq, Zacharie
last_name: Taoufiq
- first_name: Satyajit
full_name: Mahapatra, Satyajit
last_name: Mahapatra
- first_name: Hiroshi
full_name: Yamada, Hiroshi
last_name: Yamada
- first_name: Kohji
full_name: Takei, Kohji
last_name: Takei
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis
and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse
model. eLife. 2022;11. doi:10.7554/eLife.73542
apa: Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z.,
… Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission
via dynamin sequestration in Alzheimer’s disease synapse model. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.73542
chicago: Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent
Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and
Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission
via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” ELife.
eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.73542.
ieee: T. Hori et al., “Microtubule assembly by tau impairs endocytosis and
neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,”
eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S,
Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis
and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse
model. eLife. 11, e73542.
mla: Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and
Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.”
ELife, vol. 11, e73542, eLife Sciences Publications, 2022, doi:10.7554/eLife.73542.
short: T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra,
H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).
date_created: 2022-05-29T22:01:54Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:15:49Z
day: '05'
ddc:
- '616'
department:
- _id: RySh
doi: 10.7554/eLife.73542
external_id:
isi:
- '000876231600001'
pmid:
- '35471147 '
file:
- access_level: open_access
checksum: ccddbd167e00ff8375f12998af497152
content_type: application/pdf
creator: cchlebak
date_created: 2022-05-30T08:09:16Z
date_updated: 2022-05-30T08:09:16Z
file_id: '11421'
file_name: elife-73542-v2.pdf
file_size: 2466296
relation: main_file
success: 1
file_date_updated: 2022-05-30T08:09:16Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin
sequestration in Alzheimer's disease synapse model
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '11420'
abstract:
- lang: eng
text: 'Understanding the properties of neural networks trained via stochastic gradient
descent (SGD) is at the heart of the theory of deep learning. In this work, we
take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD
for a univariate regularized regression problem. Our main result is that SGD with
vanishingly small noise injected in the gradients is biased towards a simple solution:
at convergence, the ReLU network implements a piecewise linear map of the inputs,
and the number of “knot” points -- i.e., points where the tangent of the ReLU
network estimator changes -- between two consecutive training inputs is at most
three. In particular, as the number of neurons of the network grows, the SGD dynamics
is captured by the solution of a gradient flow and, at convergence, the distribution
of the weights approaches the unique minimizer of a related free energy, which
has a Gibbs form. Our key technical contribution consists in the analysis of the
estimator resulting from this minimizer: we show that its second derivative vanishes
everywhere, except at some specific locations which represent the “knot” points.
We also provide empirical evidence that knots at locations distinct from the data
points might occur, as predicted by our theory.'
acknowledgement: "We would like to thank Mert Pilanci for several exploratory discussions
in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et
al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko
and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev
acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765
Research Center for Informatics.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
- first_name: Vyacheslav
full_name: Kungurtsev, Vyacheslav
last_name: Kungurtsev
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear
solutions for wide ReLU networks. Journal of Machine Learning Research.
2022;23(130):1-55.
apa: Shevchenko, A., Kungurtsev, V., & Mondelli, M. (2022). Mean-field analysis
of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning
Research. Journal of Machine Learning Research.
chicago: Shevchenko, Aleksandr, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field
Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” Journal of
Machine Learning Research. Journal of Machine Learning Research, 2022.
ieee: A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise
linear solutions for wide ReLU networks,” Journal of Machine Learning Research,
vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.
ista: Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise
linear solutions for wide ReLU networks. Journal of Machine Learning Research.
23(130), 1–55.
mla: Shevchenko, Aleksandr, et al. “Mean-Field Analysis of Piecewise Linear Solutions
for Wide ReLU Networks.” Journal of Machine Learning Research, vol. 23,
no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.
short: A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research
23 (2022) 1–55.
date_created: 2022-05-29T22:01:54Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2024-09-10T13:03:17Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
- _id: DaAl
external_id:
arxiv:
- '2111.02278'
file:
- access_level: open_access
checksum: d4ff5d1affb34848b5c5e4002483fc62
content_type: application/pdf
creator: cchlebak
date_created: 2022-05-30T08:22:55Z
date_updated: 2022-05-30T08:22:55Z
file_id: '11422'
file_name: 21-1365.pdf
file_size: 1521701
relation: main_file
success: 1
file_date_updated: 2022-05-30T08:22:55Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '130'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1-55
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
issn:
- 1532-4435
publication_status: published
publisher: Journal of Machine Learning Research
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://www.jmlr.org/papers/v23/21-1365.html
scopus_import: '1'
status: public
title: Mean-field analysis of piecewise linear solutions for wide ReLU networks
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 23
year: '2022'
...
---
_id: '11428'
abstract:
- lang: eng
text: The medial axis of a set consists of the points in the ambient space without
a unique closest point on the original set. Since its introduction, the medial
axis has been used extensively in many applications as a method of computing a
topologically equivalent skeleton. Unfortunately, one limiting factor in the use
of the medial axis of a smooth manifold is that it is not necessarily topologically
stable under small perturbations of the manifold. To counter these instabilities
various prunings of the medial axis have been proposed. Here, we examine one type
of pruning, called burning. Because of the good experimental results, it was hoped
that the burning method of simplifying the medial axis would be stable. In this
work we show a simple example that dashes such hopes based on Bing’s house with
two rooms, demonstrating an isotopy of a shape where the medial axis goes from
collapsible to non-collapsible.
acknowledgement: 'Partially supported by the DFG Collaborative Research Center TRR
109, “Discretization in Geometry and Dynamics” and the European Research Council
(ERC), grant no. 788183, “Alpha Shape Theory Extended”. Erin Chambers: Supported
in part by the National Science Foundation through grants DBI-1759807, CCF-1907612,
and CCF-2106672. Mathijs Wintraecken: Supported by the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 754411. The Austrian science fund (FWF) M-3073 Acknowledgements We thank André
Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early
discussions on this work. We also thank Lu Liu, Yajie Yan and Tao Ju for sharing
code to generate the examples.'
article_processing_charge: No
author:
- first_name: Erin
full_name: Chambers, Erin
last_name: Chambers
- first_name: Christopher D
full_name: Fillmore, Christopher D
id: 35638A5C-AAC7-11E9-B0BF-5503E6697425
last_name: Fillmore
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. A cautionary tale:
Burning the medial axis is unstable. In: Goaoc X, Kerber M, eds. 38th International
Symposium on Computational Geometry. Vol 224. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2022:66:1-66:9. doi:10.4230/LIPIcs.SoCG.2022.66'
apa: 'Chambers, E., Fillmore, C. D., Stephenson, E. R., & Wintraecken, M. (2022).
A cautionary tale: Burning the medial axis is unstable. In X. Goaoc & M. Kerber
(Eds.), 38th International Symposium on Computational Geometry (Vol. 224,
p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SoCG.2022.66'
chicago: 'Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs
Wintraecken. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” In 38th
International Symposium on Computational Geometry, edited by Xavier Goaoc
and Michael Kerber, 224:66:1-66:9. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2022. https://doi.org/10.4230/LIPIcs.SoCG.2022.66.'
ieee: 'E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary
tale: Burning the medial axis is unstable,” in 38th International Symposium
on Computational Geometry, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9.'
ista: 'Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. 2022. A cautionary
tale: Burning the medial axis is unstable. 38th International Symposium on Computational
Geometry. SoCG: Symposium on Computational GeometryLIPIcs vol. 224, 66:1-66:9.'
mla: 'Chambers, Erin, et al. “A Cautionary Tale: Burning the Medial Axis Is Unstable.”
38th International Symposium on Computational Geometry, edited by Xavier
Goaoc and Michael Kerber, vol. 224, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2022, p. 66:1-66:9, doi:10.4230/LIPIcs.SoCG.2022.66.'
short: E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, X. Goaoc,
M. Kerber (Eds.), 38th International Symposium on Computational Geometry, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9.
conference:
end_date: 2022-06-10
location: Berlin, Germany
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2022-06-07
date_created: 2022-06-01T14:18:04Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-02-21T09:50:52Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2022.66
ec_funded: 1
editor:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
file:
- access_level: open_access
checksum: b25ce40fade4ebc0bcaae176db4f5f1f
content_type: application/pdf
creator: dernst
date_created: 2022-06-07T07:58:30Z
date_updated: 2022-06-07T07:58:30Z
file_id: '11437'
file_name: 2022_LIPICs_Chambers.pdf
file_size: 17580705
relation: main_file
success: 1
file_date_updated: 2022-06-07T07:58:30Z
has_accepted_license: '1'
intvolume: ' 224'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 66:1-66:9
project:
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 38th International Symposium on Computational Geometry
publication_identifier:
isbn:
- 978-3-95977-227-3
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
series_title: LIPIcs
status: public
title: 'A cautionary tale: Burning the medial axis is unstable'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 224
year: '2022'
...
---
_id: '11429'
abstract:
- lang: eng
text: "This book constitutes the refereed proceedings of the 18th International
Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held
in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with
6 short papers in the volume were carefully reviewed and selected from 16 submissions.
\ The papers cover topics that range from mobile GIS and Location-Based Services
to Spatial Information Retrieval and Wireless Sensor Networks."
alternative_title:
- LNCS
article_processing_charge: No
citation:
ama: 'Karimipour F, Storandt S, eds. Web and Wireless Geographical Information
Systems. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:10.1007/978-3-031-06245-2'
apa: 'Karimipour, F., & Storandt, S. (Eds.). (2022). Web and Wireless Geographical
Information Systems (1st ed., Vol. 13238). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-06245-2'
chicago: 'Karimipour, Farid, and Sabine Storandt, eds. Web and Wireless Geographical
Information Systems. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-031-06245-2.'
ieee: 'F. Karimipour and S. Storandt, Eds., Web and Wireless Geographical Information
Systems, 1st ed., vol. 13238. Cham: Springer Nature, 2022.'
ista: 'Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information
Systems 1st ed., Cham: Springer Nature, 153p.'
mla: Karimipour, Farid, and Sabine Storandt, editors. Web and Wireless Geographical
Information Systems. 1st ed., vol. 13238, Springer Nature, 2022, doi:10.1007/978-3-031-06245-2.
short: F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information
Systems, 1st ed., Springer Nature, Cham, 2022.
date_created: 2022-06-02T05:40:53Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2022-06-02T05:56:22Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-031-06245-2
edition: '1'
editor:
- first_name: Farid
full_name: Karimipour, Farid
id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425
last_name: Karimipour
orcid: 0000-0001-6746-4174
- first_name: Sabine
full_name: Storandt, Sabine
last_name: Storandt
intvolume: ' 13238'
language:
- iso: eng
month: '05'
oa_version: None
page: '153'
place: Cham
publication_identifier:
eisbn:
- '9783031062452'
eissn:
- 1611-3349
isbn:
- '9783031062445'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Web and Wireless Geographical Information Systems
type: book_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13238
year: '2022'
...
---
_id: '11432'
abstract:
- lang: eng
text: "This paper proposes a method for simulating liquids in large bodies of water
by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator.
The surface wave simulation uses the equivalent sources method (ESM) to efficiently
animate large bodies of water with precisely controllable wave propagation behavior.
The 3D liquid simulator animates complex non-linear fluid behaviors like splashes
and breaking waves using off-the-shelf simulators using FLIP or the level set
method with semi-Lagrangian advection.\r\nWe combine the two approaches by using
the 3D solver to animate localized non-linear behaviors, and the 2D wave solver
to animate larger regions with linear surface physics. We use the surface motion
from the 3D solver as boundary conditions for 2D surface wave simulator, and we
use the velocity and surface heights from the 2D surface wave simulator as boundary
conditions for the 3D fluid simulation. We also introduce a novel technique for
removing visual artifacts caused by numerical errors in 3D fluid solvers: we use
experimental data to estimate the artificial dispersion caused by the 3D solver
and we then carefully tune the wave speeds of the 2D solver to match it, effectively
eliminating any differences in wave behavior across the boundary. To the best
of our knowledge, this is the first time such a empirically driven error compensation
approach has been used to remove coupling errors from a physics simulator.\r\nOur
coupled simulation approach leverages the strengths of each simulation technique,
animating large environments with seamless transitions between 2D and 3D physics."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We wish to thank the anonymous reviewers and the members of the Visual
Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback.
This research was supported by the Scientific Service Units (SSU) of IST Austria
through resources provided by Scientific Computing. This project has received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme under grant agreement No. 638176.
article_processing_charge: No
article_type: original
author:
- first_name: Camille
full_name: Schreck, Camille
id: 2B14B676-F248-11E8-B48F-1D18A9856A87
last_name: Schreck
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation
for large scale water surface animation using the equivalent sources method. Computer
Graphics Forum. 2022;41(2):343-353. doi:10.1111/cgf.14478
apa: Schreck, C., & Wojtan, C. (2022). Coupling 3D liquid simulation with 2D
wave propagation for large scale water surface animation using the equivalent
sources method. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14478
chicago: Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with
2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent
Sources Method.” Computer Graphics Forum. Wiley, 2022. https://doi.org/10.1111/cgf.14478.
ieee: C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation
for large scale water surface animation using the equivalent sources method,”
Computer Graphics Forum, vol. 41, no. 2. Wiley, pp. 343–353, 2022.
ista: Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation
for large scale water surface animation using the equivalent sources method. Computer
Graphics Forum. 41(2), 343–353.
mla: Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D
Wave Propagation for Large Scale Water Surface Animation Using the Equivalent
Sources Method.” Computer Graphics Forum, vol. 41, no. 2, Wiley, 2022,
pp. 343–53, doi:10.1111/cgf.14478.
short: C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353.
date_created: 2022-06-05T22:01:49Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-02T06:44:05Z
day: '01'
department:
- _id: ChWo
doi: 10.1111/cgf.14478
ec_funded: 1
external_id:
isi:
- '000802723900027'
intvolume: ' 41'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03641349/
month: '05'
oa: 1
oa_version: Submitted Version
page: 343-353
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: Computer Graphics Forum
publication_identifier:
eissn:
- 1467-8659
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coupling 3D liquid simulation with 2D wave propagation for large scale water
surface animation using the equivalent sources method
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2022'
...
---
_id: '11435'
abstract:
- lang: eng
text: 'We introduce a new variant of quantitative Helly-type theorems: the minimal
homothetic distance of the intersection of a family of convex sets to the intersection
of a subfamily of a fixed size. As an application, we establish the following
quantitative Helly-type result for the diameter. If $K$ is the intersection of
finitely many convex bodies in $\mathbb{R}^d$, then one can select $2d$ of these
bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously
known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25],
is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$
conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982),
pp. 109--114] cannot be improved. The bounds above follow from our key result
that concerns sparse approximation of a convex polytope by the convex hull of
a well-chosen subset of its vertices: Assume that $Q \subset {\mathbb R}^d$ is
a polytope whose centroid is the origin. Then there exist at most 2d vertices
of $Q$ whose convex hull $Q^{\prime \prime}$ satisfies $Q \subset - 8d^3 Q^{\prime
\prime}.$'
acknowledgement: "G.I. acknowledges the financial support from the Ministry of Educational
and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926.
M.N. was supported by the National Research, Development and Innovation Fund (NRDI)
grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian
Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06
program provided by the NRDI."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Marton
full_name: Naszodi, Marton
last_name: Naszodi
citation:
ama: 'Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet.
SIAM Journal on Discrete Mathematics. 2022;36(2):951-957. doi:10.1137/21M1403308'
apa: 'Ivanov, G., & Naszodi, M. (2022). A quantitative Helly-type theorem: Containment
in a homothet. SIAM Journal on Discrete Mathematics. Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/21M1403308'
chicago: 'Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem:
Containment in a Homothet.” SIAM Journal on Discrete Mathematics. Society
for Industrial and Applied Mathematics, 2022. https://doi.org/10.1137/21M1403308.'
ieee: 'G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment
in a homothet,” SIAM Journal on Discrete Mathematics, vol. 36, no. 2. Society
for Industrial and Applied Mathematics, pp. 951–957, 2022.'
ista: 'Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment
in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.'
mla: 'Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment
in a Homothet.” SIAM Journal on Discrete Mathematics, vol. 36, no. 2, Society
for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:10.1137/21M1403308.'
short: G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957.
date_created: 2022-06-05T22:01:50Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2023-10-18T06:58:03Z
day: '11'
department:
- _id: UlWa
doi: 10.1137/21M1403308
external_id:
arxiv:
- '2103.04122'
isi:
- '000793158200002'
intvolume: ' 36'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2103.04122'
month: '04'
oa: 1
oa_version: Preprint
page: 951-957
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
issn:
- 0895-4801
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A quantitative Helly-type theorem: Containment in a homothet'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2022'
...
---
_id: '11438'
abstract:
- lang: eng
text: Lasers with well-controlled relative frequencies are indispensable for many
applications in science and technology. We present a frequency-offset locking
method for lasers based on beat-frequency discrimination utilizing hybrid electronic
LC filters. The method is specifically designed for decoupling the tightness of
the lock from the broadness of its capture range. The presented demonstration
locks two free-running diode lasers at 780 nm with a 5.5-GHz offset. It displays
an offset frequency instability below 55 Hz for time scales in excess of 1000
s and a minimum of 12 Hz at 10-s averaging. The performance is complemented with
a 190-MHz lock-capture range, a tuning range of up to 1 GHz, and a frequency ramp
agility of 200kHz/μs.
acknowledgement: This work was supported by IST Austria. The authors thank Yueheng
Shi for technical contributions.
article_number: '054031'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Vyacheslav
full_name: Li, Vyacheslav
id: 3A4FAA92-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Fritz R
full_name: Diorico, Fritz R
id: 2E054C4C-F248-11E8-B48F-1D18A9856A87
last_name: Diorico
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: Li V, Diorico FR, Hosten O. Laser frequency-offset locking at 10-Hz-level instability
using hybrid electronic filters. Physical Review Applied. 2022;17(5). doi:10.1103/physrevapplied.17.054031
apa: Li, V., Diorico, F. R., & Hosten, O. (2022). Laser frequency-offset locking
at 10-Hz-level instability using hybrid electronic filters. Physical Review
Applied. American Physical Society. https://doi.org/10.1103/physrevapplied.17.054031
chicago: Li, Vyacheslav, Fritz R Diorico, and Onur Hosten. “Laser Frequency-Offset
Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” Physical
Review Applied. American Physical Society, 2022. https://doi.org/10.1103/physrevapplied.17.054031.
ieee: V. Li, F. R. Diorico, and O. Hosten, “Laser frequency-offset locking at 10-Hz-level
instability using hybrid electronic filters,” Physical Review Applied,
vol. 17, no. 5. American Physical Society, 2022.
ista: Li V, Diorico FR, Hosten O. 2022. Laser frequency-offset locking at 10-Hz-level
instability using hybrid electronic filters. Physical Review Applied. 17(5), 054031.
mla: Li, Vyacheslav, et al. “Laser Frequency-Offset Locking at 10-Hz-Level Instability
Using Hybrid Electronic Filters.” Physical Review Applied, vol. 17, no.
5, 054031, American Physical Society, 2022, doi:10.1103/physrevapplied.17.054031.
short: V. Li, F.R. Diorico, O. Hosten, Physical Review Applied 17 (2022).
date_created: 2022-06-07T08:07:59Z
date_published: 2022-05-19T00:00:00Z
date_updated: 2023-08-03T07:18:34Z
day: '19'
department:
- _id: GradSch
- _id: OnHo
doi: 10.1103/physrevapplied.17.054031
external_id:
arxiv:
- '2111.13194'
isi:
- '000880670300001'
intvolume: ' 17'
isi: 1
issue: '5'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2111.13194'
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
issn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic
filters
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2022'
...
---
_id: '11440'
abstract:
- lang: eng
text: To compute the persistent homology of a grayscale digital image one needs
to build a simplicial or cubical complex from it. For cubical complexes, the two
commonly used constructions (corresponding to direct and indirect digital adjacencies)
can give different results for the same image. The two constructions are almost
dual to each other, and we use this relationship to extend and modify the cubical
complexes to become dual filtered cell complexes. We derive a general relationship
between the persistent homology of two dual filtered cell complexes, and also
establish how various modifications to a filtered complex change the persistence
diagram. Applying these results to images, we derive a method to transform the
persistence diagram computed using one type of cubical complex into a persistence
diagram for the other construction. This means software for computing persistent
homology from images can now be easily adapted to produce results for either of
the two cubical complex constructions without additional low-level code implementation.
acknowledgement: This project started during the Women in Computational Topology workshop
held in Canberra in July of 2019. All authors are very grateful for its organisation
and the financial support for the workshop from the Mathematical Sciences Institute
at ANU, the US National Science Foundation through the award CCF-1841455, the Australian
Mathematical Sciences Institute and the Association for Women in Mathematics. AG
is supported by the Swiss National Science Foundation grant CRSII5_177237. TH is
supported by the European Research Council (ERC) Horizon 2020 project “Alpha Shape
Theory Extended” No. 788183. KM is supported by the ERC Horizon 2020 research and
innovation programme under the Marie Sklodowska-Curie grant agreement No. 859860.
VR was supported by Australian Research Council Future Fellowship FT140100604 during
the early stages of this project.
alternative_title:
- Association for Women in Mathematics Series
article_processing_charge: No
arxiv: 1
author:
- first_name: Bea
full_name: Bleile, Bea
last_name: Bleile
- first_name: Adélie
full_name: Garin, Adélie
last_name: Garin
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Kelly
full_name: Maggs, Kelly
last_name: Maggs
- first_name: Vanessa
full_name: Robins, Vanessa
last_name: Robins
citation:
ama: 'Bleile B, Garin A, Heiss T, Maggs K, Robins V. The persistent homology of
dual digital image constructions. In: Gasparovic E, Robins V, Turner K, eds. Research
in Computational Topology 2. Vol 30. 1st ed. AWMS. Cham: Springer Nature;
2022:1-26. doi:10.1007/978-3-030-95519-9_1'
apa: 'Bleile, B., Garin, A., Heiss, T., Maggs, K., & Robins, V. (2022). The
persistent homology of dual digital image constructions. In E. Gasparovic, V.
Robins, & K. Turner (Eds.), Research in Computational Topology 2 (1st
ed., Vol. 30, pp. 1–26). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-95519-9_1'
chicago: 'Bleile, Bea, Adélie Garin, Teresa Heiss, Kelly Maggs, and Vanessa Robins.
“The Persistent Homology of Dual Digital Image Constructions.” In Research
in Computational Topology 2, edited by Ellen Gasparovic, Vanessa Robins, and
Katharine Turner, 1st ed., 30:1–26. AWMS. Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-030-95519-9_1.'
ieee: 'B. Bleile, A. Garin, T. Heiss, K. Maggs, and V. Robins, “The persistent homology
of dual digital image constructions,” in Research in Computational Topology
2, 1st ed., vol. 30, E. Gasparovic, V. Robins, and K. Turner, Eds. Cham: Springer
Nature, 2022, pp. 1–26.'
ista: 'Bleile B, Garin A, Heiss T, Maggs K, Robins V. 2022.The persistent homology
of dual digital image constructions. In: Research in Computational Topology 2.
Association for Women in Mathematics Series, vol. 30, 1–26.'
mla: Bleile, Bea, et al. “The Persistent Homology of Dual Digital Image Constructions.”
Research in Computational Topology 2, edited by Ellen Gasparovic et al.,
1st ed., vol. 30, Springer Nature, 2022, pp. 1–26, doi:10.1007/978-3-030-95519-9_1.
short: B. Bleile, A. Garin, T. Heiss, K. Maggs, V. Robins, in:, E. Gasparovic, V.
Robins, K. Turner (Eds.), Research in Computational Topology 2, 1st ed., Springer
Nature, Cham, 2022, pp. 1–26.
date_created: 2022-06-07T08:21:11Z
date_published: 2022-01-27T00:00:00Z
date_updated: 2022-06-07T08:32:42Z
day: '27'
department:
- _id: HeEd
doi: 10.1007/978-3-030-95519-9_1
ec_funded: 1
edition: '1'
editor:
- first_name: Ellen
full_name: Gasparovic, Ellen
last_name: Gasparovic
- first_name: Vanessa
full_name: Robins, Vanessa
last_name: Robins
- first_name: Katharine
full_name: Turner, Katharine
last_name: Turner
external_id:
arxiv:
- '2102.11397'
intvolume: ' 30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2102.11397'
month: '01'
oa: 1
oa_version: Preprint
page: 1-26
place: Cham
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
publication: Research in Computational Topology 2
publication_identifier:
eisbn:
- '9783030955199'
isbn:
- '9783030955182'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: AWMS
status: public
title: The persistent homology of dual digital image constructions
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2022'
...
---
_id: '11442'
abstract:
- lang: eng
text: "Enabling additive manufacturing to employ a wide range of novel, functional
materials can be a major boost to this technology. However, making such materials
printable requires painstaking trial-and-error by an expert operator,\r\nas they
typically tend to exhibit peculiar rheological or hysteresis properties. Even
in the case of successfully finding the process parameters, there is no guarantee
of print-to-print consistency due to material differences between batches. These
challenges make closed-loop feedback an attractive option where the process parameters
are adjusted on-the-fly. There are several challenges for designing an efficient
controller: the deposition parameters are complex and highly coupled, artifacts
occur after long time horizons, simulating the deposition is computationally costly,
and learning on hardware is intractable. In this work, we demonstrate the feasibility
of learning a closed-loop control policy for additive manufacturing using reinforcement
learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient
as long as it allows learning the behavioral patterns of deposition that translate
to real-world experiences. In combination with reinforcement learning, our model
can be used to discover control policies that outperform\r\nbaseline controllers.
Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase
this by applying our control policy in-vivo on a single-layer, direct ink writing
printer. "
acknowledgement: "This work is graciously supported by the following grant agencies:
FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767),
NSF (Grant IIS-181507).\r\n"
article_number: '112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
- first_name: Michael
full_name: Foshey, Michael
last_name: Foshey
- first_name: Jie
full_name: Xu, Jie
last_name: Xu
- first_name: Timothy
full_name: Erps, Timothy
last_name: Erps
- first_name: Vahid
full_name: Babaei, Vahid
last_name: Babaei
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Szymon
full_name: Rusinkiewicz, Szymon
last_name: Rusinkiewicz
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing
via reinforcement learning. ACM Transactions on Graphics. 2022;41(4). doi:10.1145/3528223.3530144
apa: Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel,
B. (2022). Closed-loop control of direct ink writing via reinforcement learning.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3528223.3530144
chicago: Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei,
Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop
Control of Direct Ink Writing via Reinforcement Learning.” ACM Transactions
on Graphics. Association for Computing Machinery, 2022. https://doi.org/10.1145/3528223.3530144.
ieee: M. Piovarci et al., “Closed-loop control of direct ink writing via
reinforcement learning,” ACM Transactions on Graphics, vol. 41, no. 4.
Association for Computing Machinery, 2022.
ista: Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik
W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement
learning. ACM Transactions on Graphics. 41(4), 112.
mla: Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement
Learning.” ACM Transactions on Graphics, vol. 41, no. 4, 112, Association
for Computing Machinery, 2022, doi:10.1145/3528223.3530144.
short: M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz,
W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).
date_created: 2022-06-10T06:41:47Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-05-31T12:38:21Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3528223.3530144
ec_funded: 1
external_id:
arxiv:
- '2201.11819'
file:
- access_level: open_access
checksum: 27f6fe41c6ff84d50445cc9b0176d45b
content_type: application/pdf
creator: dernst
date_created: 2022-06-28T08:32:58Z
date_updated: 2022-06-28T08:32:58Z
file_id: '11467'
file_name: 2022_ACM_acceptedversion_Piovarci.pdf
file_size: 33994829
relation: main_file
success: 1
file_date_updated: 2022-06-28T08:32:58Z
has_accepted_license: '1'
intvolume: ' 41'
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/
status: public
title: Closed-loop control of direct ink writing via reinforcement learning
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: 41
year: '2022'
...
---
_id: '11443'
abstract:
- lang: eng
text: Sometimes, it is possible to represent a complicated polytope as a projection
of a much simpler polytope. To quantify this phenomenon, the extension complexity
of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional)
polytope from which P can be obtained as a (linear) projection. This notion is
motivated by its relevance to combinatorial optimisation, and has been studied
intensively for various specific polytopes associated with important optimisation
problems. In this paper we study extension complexity as a parameter of general
polytopes, more specifically considering various families of low-dimensional polytopes.
First, we prove that for a fixed dimension d, the extension complexity of a random
d-dimensional polytope (obtained as the convex hull of random points in a ball
or on a sphere) is typically on the order of the square root of its number of
vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie
on a circle) has extension complexity at most 24√n. This bound is tight up to
the constant factor 24. Finally, we show that there exists an no(1)-dimensional
polytope with at most n vertices and extension complexity n1−o(1). Our theorems
are proved with a range of different techniques, which we hope will be of further
interest.
acknowledgement: "The research of the first author was supported by SNSF Project 178493
and NSF Award DMS-1953990. The research of the second author supported by NSF Award
DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176,
NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum
Fund. "
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
- first_name: Yufei
full_name: Zhao, Yufei
last_name: Zhao
citation:
ama: Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes.
Transactions of the American Mathematical Society. 2022;375(6):4209-4250.
doi:10.1090/tran/8614
apa: Kwan, M. A., Sauermann, L., & Zhao, Y. (2022). Extension complexity of
low-dimensional polytopes. Transactions of the American Mathematical Society.
American Mathematical Society. https://doi.org/10.1090/tran/8614
chicago: Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity
of Low-Dimensional Polytopes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2022. https://doi.org/10.1090/tran/8614.
ieee: M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional
polytopes,” Transactions of the American Mathematical Society, vol. 375,
no. 6. American Mathematical Society, pp. 4209–4250, 2022.
ista: Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional
polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.
mla: Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.”
Transactions of the American Mathematical Society, vol. 375, no. 6, American
Mathematical Society, 2022, pp. 4209–50, doi:10.1090/tran/8614.
short: M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical
Society 375 (2022) 4209–4250.
date_created: 2022-06-12T22:01:45Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T07:17:37Z
day: '01'
department:
- _id: MaKw
doi: 10.1090/tran/8614
external_id:
arxiv:
- '2006.08836'
isi:
- '000798461500001'
intvolume: ' 375'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2006.08836'
month: '06'
oa: 1
oa_version: Preprint
page: 4209-4250
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6850
issn:
- 0002-9947
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extension complexity of low-dimensional polytopes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2022'
...
---
_id: '11444'
abstract:
- lang: eng
text: "This article investigates library-related documents written by Gerard van
Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library
of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through
a textual analysis. Handwritten letters were deconstructed in terms of their appearance,
layout, and tone in order to mine them for meaning. Furthermore, the contents
were examined for library matters such as censorship, catalogues, and collection
development. The Imperial Court Library held a prominent role as a repository
for rare and valuable works, later becoming the National Library of Austria.\r\nGerard
van Swieten’s work as a librarian tends to be overlooked, perhaps because he is
better known as the private physician of Maria Theresia, as well as a medical
reformer. Nevertheless, he was a hard-working chief librarian deeply involved
in all aspects of librarianship. Van Swieten endorsed modern scientific works,
which were otherwise banned officially by the censorship commission, for the use
of scholars in the library, expanded the collection by acquiring books through
his network of scholars and publishers, and reissued library catalogues. He also
provided for the comfort of users in the library reading room, at a time when
such considerations were unusual. In conclusion, a proposal is made that van Swieten
viewed his role as librarian with some importance and pride."
article_processing_charge: No
article_type: original
author:
- first_name: Clara A
full_name: Chlebak, Clara A
id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
last_name: Chlebak
orcid: 0000-0002-3385-3865
- first_name: Peter H.
full_name: Reid, Peter H.
last_name: Reid
citation:
ama: 'Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library
correspondence. Library and Information History. 2022;38(1):23-41. doi:10.3366/lih.2022.0097'
apa: 'Chlebak, C. A., & Reid, P. H. (2022). From the prefect’s desk: Gerard
van Swieten’s library correspondence. Library and Information History.
Edinburgh University Press. https://doi.org/10.3366/lih.2022.0097'
chicago: 'Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard
van Swieten’s Library Correspondence.” Library and Information History.
Edinburgh University Press, 2022. https://doi.org/10.3366/lih.2022.0097.'
ieee: 'C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s
library correspondence,” Library and Information History, vol. 38, no.
1. Edinburgh University Press, pp. 23–41, 2022.'
ista: 'Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s
library correspondence. Library and Information History. 38(1), 23–41.'
mla: 'Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van
Swieten’s Library Correspondence.” Library and Information History, vol.
38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:10.3366/lih.2022.0097.'
short: C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.
date_created: 2022-06-12T22:01:45Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2023-02-21T09:51:29Z
day: '01'
department:
- _id: E-Lib
doi: 10.3366/lih.2022.0097
intvolume: ' 38'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://rgu-repository.worktribe.com/output/1635939
month: '04'
oa: 1
oa_version: Submitted Version
page: 23-41
publication: Library and Information History
publication_identifier:
eissn:
- 1758-3497
issn:
- 1758-3489
publication_status: published
publisher: Edinburgh University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the prefect’s desk: Gerard van Swieten’s library correspondence'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 84
year: '2022'
...
---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:20:15Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '11449'
abstract:
- lang: eng
text: Mutations are acquired frequently, such that each cell's genome inscribes
its history of cell divisions. Common genomic alterations involve loss of heterozygosity
(LOH). LOH accumulates throughout the genome, offering large encoding capacity
for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq)
of mouse brain cells, we found that LOH events spanning multiple genes are revealed
as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide
variants (SNVs). We simultaneously inferred cell lineage and marked developmental
time points based on X chromosome inactivation and the total number of LOH events
while identifying cell types from gene expression patterns. Our results are consistent
with progenitor cells giving rise to multiple cortical cell types through stereotyped
expansion and distinct waves of neurogenesis. This type of retrospective analysis
could be incorporated into scRNA-seq pipelines and, compared with experimental
approaches for determining lineage in model organisms, is applicable where genetic
engineering is prohibited, such as humans.
acknowledgement: D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk
Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory
to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University
of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b]
life science call grant (C13-002) and the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program 725780 LinPro
to S.H.
article_processing_charge: No
article_type: original
author:
- first_name: Donovan J.
full_name: Anderson, Donovan J.
last_name: Anderson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Aaron
full_name: Mckenna, Aaron
last_name: Mckenna
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Marshall S.
full_name: Horwitz, Marshall S.
last_name: Horwitz
citation:
ama: Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous
brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical
development. Cell Systems. 2022;13(6):438-453.e5. doi:10.1016/j.cels.2022.03.006
apa: Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &
Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by
scRNA-seq reveals stereotyped cortical development. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2022.03.006
chicago: Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon
Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage
Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” Cell Systems.
Elsevier, 2022. https://doi.org/10.1016/j.cels.2022.03.006.
ieee: D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M.
S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq
reveals stereotyped cortical development,” Cell Systems, vol. 13, no. 6.
Elsevier, p. 438–453.e5, 2022.
ista: Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022.
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped
cortical development. Cell Systems. 13(6), 438–453.e5.
mla: Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined
by ScRNA-Seq Reveals Stereotyped Cortical Development.” Cell Systems, vol.
13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:10.1016/j.cels.2022.03.006.
short: D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz,
Cell Systems 13 (2022) 438–453.e5.
date_created: 2022-06-19T22:01:57Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2023-08-03T07:19:43Z
day: '15'
department:
- _id: SiHi
doi: 10.1016/j.cels.2022.03.006
ec_funded: 1
external_id:
isi:
- '000814124400002'
pmid:
- '35452605'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cels.2022.03.006
month: '06'
oa: 1
oa_version: Published Version
page: 438-453.e5
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped
cortical development
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '11451'
abstract:
- lang: eng
text: The precursor conversion chemistry and surface chemistry of Cu3N and Cu3PdN
nanocrystals are unknown or contested. Here, we first obtain phase-pure, colloidally
stable nanocubes. Second, we elucidate the pathway by which copper(II) nitrate
and oleylamine form Cu3N. We find that oleylamine is both a reductant and a nitrogen
source. Oleylamine is oxidized by nitrate to a primary aldimine, which reacts
further with excess oleylamine to a secondary aldimine, eliminating ammonia. Ammonia
reacts with CuI to form Cu3N. Third, we investigated the surface chemistry and
find a mixed ligand shell of aliphatic amines and carboxylates (formed in situ).
While the carboxylates appear tightly bound, the amines are easily desorbed from
the surface. Finally, we show that doping with palladium decreases the band gap
and the material becomes semi-metallic. These results bring insight into the chemistry
of metal nitrides and might help the development of other metal nitride nanocrystals.
acknowledgement: 'J.D.R. and M.P. acknowledge the SNF Eccellenza funding scheme (project
number: 194172). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz
Association HGF, for the provision of experimental facilities. Parts of this research
were carried out at beamline P21.1, PETRA III. We thank Dr. Soham Banerjee for acquiring
the PDF data and helpful advice. A.R. acknowledges the support from the Analytical
Chemistry Trust Fund for her CAMS-UK Fellowship. C.K. acknowledges the support from
the Department of Chemistry, UCL. The authors acknowledge Dr Stephan Lany from NREL
for providing the Cu3N DFT calculations. The authors thank Prof. Raymond Schaak
and Dr. Robert William Lord for helpful advice and suggestions regarding the purification
procedure. Open access funding provided by Universitat Basel.'
article_number: e202207013
article_processing_charge: No
article_type: original
author:
- first_name: Mahsa
full_name: Parvizian, Mahsa
last_name: Parvizian
- first_name: Alejandra
full_name: Duràn Balsa, Alejandra
last_name: Duràn Balsa
- first_name: Rohan
full_name: Pokratath, Rohan
last_name: Pokratath
- first_name: Curran
full_name: Kalha, Curran
last_name: Kalha
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Dietger
full_name: Van Den Eynden, Dietger
last_name: Van Den Eynden
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Anna
full_name: Regoutz, Anna
last_name: Regoutz
- first_name: Jonathan
full_name: De Roo, Jonathan
last_name: De Roo
citation:
ama: Parvizian M, Duràn Balsa A, Pokratath R, et al. The chemistry of Cu₃N and Cu₃PdN
nanocrystals. Angewandte Chemie - International Edition. 2022;61(31). doi:10.1002/anie.202207013
apa: Parvizian, M., Duràn Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van Den
Eynden, D., … De Roo, J. (2022). The chemistry of Cu₃N and Cu₃PdN nanocrystals.
Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.202207013
chicago: Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha,
Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan
De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” Angewandte Chemie
- International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202207013.
ieee: M. Parvizian et al., “The chemistry of Cu₃N and Cu₃PdN nanocrystals,”
Angewandte Chemie - International Edition, vol. 61, no. 31. Wiley, 2022.
ista: Parvizian M, Duràn Balsa A, Pokratath R, Kalha C, Lee S, Van Den Eynden D,
Ibáñez M, Regoutz A, De Roo J. 2022. The chemistry of Cu₃N and Cu₃PdN nanocrystals.
Angewandte Chemie - International Edition. 61(31), e202207013.
mla: Parvizian, Mahsa, et al. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” Angewandte
Chemie - International Edition, vol. 61, no. 31, e202207013, Wiley, 2022,
doi:10.1002/anie.202207013.
short: M. Parvizian, A. Duràn Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van Den
Eynden, M. Ibáñez, A. Regoutz, J. De Roo, Angewandte Chemie - International Edition
61 (2022).
date_created: 2022-06-19T22:01:58Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T07:19:12Z
day: '01'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1002/anie.202207013
external_id:
isi:
- '000811084000001'
pmid:
- '35612297'
file:
- access_level: open_access
checksum: 2a3ee0bb59e044b808ebe85cd94ac899
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T09:29:20Z
date_updated: 2022-07-29T09:29:20Z
file_id: '11696'
file_name: 2022_AngewandteChemieInternat_Parvizian.pdf
file_size: 1303202
relation: main_file
success: 1
file_date_updated: 2022-07-29T09:29:20Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '31'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '11695'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The chemistry of Cu₃N and Cu₃PdN nanocrystals
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2022'
...
---
_id: '11456'
abstract:
- lang: eng
text: The proteomes of specialized structures, and the interactomes of proteins
of interest, provide entry points to elucidate the functions of molecular machines.
Here, we review a proximity-labeling strategy that uses the improved E. coli biotin
ligase TurboID to characterize C. elegans protein complexes. Although the focus
is on C. elegans neurons, the method is applicable regardless of cell type. We
describe detailed extraction procedures that solubilize the bulk of C. elegans
proteins and highlight the importance of tagging endogenous genes, to ensure physiological
expression levels. We review issues associated with non-specific background noise
and the importance of appropriate controls. As proof of principle, we review our
analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our
aim is to provide a detailed protocol for TurboID-based proximity labeling in
C. elegans and to highlight its potential and its limitations to characterize
protein complexes and subcellular compartments in this animal.
acknowledgement: We thank de Bono lab members for the helpful comments on the manuscript.
The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J.
Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and
Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop
and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly
sent by Dr. Dominique Glauser (University of Fribourg). This work was supported
by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z)
to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
- 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: 'Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based
Proximity Labeling. In: Yamamoto D, ed. Behavioral Neurogenetics. Vol 181.
NM. New York: Springer Nature; 2022:277-294. doi:10.1007/978-1-0716-2321-3_15'
apa: 'Artan, M., & de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons
Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), Behavioral Neurogenetics
(Vol. 181, pp. 277–294). New York: Springer Nature. https://doi.org/10.1007/978-1-0716-2321-3_15'
chicago: 'Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons
Using TurboID-Based Proximity Labeling.” In Behavioral Neurogenetics, edited
by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. https://doi.org/10.1007/978-1-0716-2321-3_15.'
ieee: 'M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using
TurboID-Based Proximity Labeling,” in Behavioral Neurogenetics, vol. 181,
D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.'
ista: 'Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based
Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.'
mla: Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons
Using TurboID-Based Proximity Labeling.” Behavioral Neurogenetics, edited
by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:10.1007/978-1-0716-2321-3_15.
short: M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer
Nature, New York, 2022, pp. 277–294.
date_created: 2022-06-20T08:10:34Z
date_published: 2022-06-04T00:00:00Z
date_updated: 2023-02-21T09:51:55Z
day: '04'
department:
- _id: MaDe
doi: 10.1007/978-1-0716-2321-3_15
ec_funded: 1
editor:
- first_name: Daisuke
full_name: Yamamoto, Daisuke
last_name: Yamamoto
intvolume: ' 181'
language:
- iso: eng
month: '06'
oa_version: None
page: 277-294
place: New York
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Behavioral Neurogenetics
publication_identifier:
eisbn:
- '9781071623213'
eissn:
- 1940-6045
isbn:
- '9781071623206'
issn:
- 0893-2336
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: NM
status: public
title: Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2022'
...
---
_id: '11459'
abstract:
- lang: eng
text: 'We present a novel approach to differential cost analysis that, given a program
revision, attempts to statically bound the difference in resource usage, or cost,
between the two program versions. Differential cost analysis is particularly interesting
because of the many compelling applications for it, such as detecting resource-use
regressions at code-review time or proving the absence of certain side-channel
vulnerabilities. One prior approach to differential cost analysis is to apply
relational reasoning that conceptually constructs a product program on which one
can over-approximate the difference in costs between the two program versions.
However, a significant challenge in any relational approach is effectively aligning
the program versions to get precise results. In this paper, our key insight is
that we can avoid the need for and the limitations of program alignment if, instead,
we bound the difference of two cost-bound summaries rather than directly bounding
the concrete cost difference. In particular, our method computes a threshold value
for the maximal difference in cost between two program versions simultaneously
using two kinds of cost-bound summaries---a potential function that evaluates
to an upper bound for the cost incurred in the first program and an anti-potential
function that evaluates to a lower bound for the cost incurred in the second.
Our method has a number of desirable properties: it can be fully automated, it
allows optimizing the threshold value on relative cost, it is suitable for programs
that are not syntactically similar, and it supports non-determinism. We have evaluated
an implementation of our approach on a number of program pairs collected from
the literature, and we find that our method computes tight threshold values on
relative cost in most examples.'
acknowledgement: "We thank Shaun Willows, Thomas Lugnet, and the Living Room Application
Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact
with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe,
and the Prime Video Automated Reasoning team for their support and helpful suggestions
throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier
version of this paper. And finally, we thank the anonymous reviewers for their useful
feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe
Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Bor-Yuh Evan
full_name: Chang, Bor-Yuh Evan
last_name: Chang
- first_name: Pauline
full_name: Bolignano, Pauline
last_name: Bolignano
- first_name: Franco
full_name: Raimondi, Franco
last_name: Raimondi
citation:
ama: 'Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis
with simultaneous potentials and anti-potentials. In: Proceedings of the 43rd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2022:442-457. doi:10.1145/3519939.3523435'
apa: 'Zikelic, D., Chang, B.-Y. E., Bolignano, P., & Raimondi, F. (2022). Differential
cost analysis with simultaneous potentials and anti-potentials. In Proceedings
of the 43rd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 442–457). San Diego, CA, United States: Association
for Computing Machinery. https://doi.org/10.1145/3519939.3523435'
chicago: Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi.
“Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.”
In Proceedings of the 43rd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 442–57. Association for Computing Machinery,
2022. https://doi.org/10.1145/3519939.3523435.
ieee: D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost
analysis with simultaneous potentials and anti-potentials,” in Proceedings
of the 43rd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, San Diego, CA, United States, 2022, pp. 442–457.
ista: 'Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis
with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 442–457.'
mla: Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials
and Anti-Potentials.” Proceedings of the 43rd ACM SIGPLAN International Conference
on Programming Language Design and Implementation, Association for Computing
Machinery, 2022, pp. 442–57, doi:10.1145/3519939.3523435.
short: D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of
the 43rd ACM SIGPLAN International Conference on Programming Language Design and
Implementation, Association for Computing Machinery, 2022, pp. 442–457.
conference:
end_date: 2022-06-17
location: San Diego, CA, United States
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2022-06-13
date_created: 2022-06-21T09:26:15Z
date_published: 2022-06-09T00:00:00Z
date_updated: 2025-07-14T09:09:54Z
day: '09'
ddc:
- '000'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1145/3519939.3523435
ec_funded: 1
external_id:
arxiv:
- '2204.00870'
isi:
- '000850435600030'
file:
- access_level: open_access
checksum: 7eb915a2ca5b5ce4729321f33b2e16e1
content_type: application/pdf
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language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 442-457
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 43rd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450392655'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differential cost analysis with simultaneous potentials and anti-potentials
tmp:
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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: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11460'
abstract:
- lang: eng
text: "Background: Proper cerebral cortical development depends on the tightly orchestrated
migration of newly born neurons from the inner ventricular and subventricular
zones to the outer cortical plate. Any disturbance in this process during prenatal
stages may lead to neuronal migration disorders (NMDs), which can vary in extent
from focal to global. Furthermore, NMDs show a substantial comorbidity with other
neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous
work demonstrated focal neuronal migration defects in mice carrying loss-of-function
alleles of the recognized autism risk gene WDFY3. However, the cellular origins
of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide
critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in
an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic
analysis with double markers (MADM). MADM technology enabled us to genetically
distinctly track and phenotypically analyze mutant and wild-type cells concomitantly
in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous
requirement of WDFY3 for accurate laminar positioning of cortical projection neurons
and elimination of mispositioned cells during early postnatal life. In addition,
we identified significant deviations in dendritic arborization, as well as synaptic
density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant
neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While
Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD
pathology that remain inaccessible to investigation in humans, like most animal
models, they do not a perfectly replicate all aspects of human ASD biology. The
lack of human data makes it indeterminate whether morphological deviations described
here apply to ASD patients or some of the other neurodevelopmental conditions
associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed
several cell autonomous requirements of WDFY3 in neuronal development that could
underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions.
The results are also consistent with findings in other ASD animal models and patients
and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity
in postnatal life."
acknowledgement: "This study was funded by NIMH R21MH115347 to KSZ. KSZ is further
supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan
de Crescenzo for early contributions to this project."
article_number: '27'
article_processing_charge: No
article_type: original
author:
- first_name: Zachary A.
full_name: Schaaf, Zachary A.
last_name: Schaaf
- first_name: Lyvin
full_name: Tat, Lyvin
last_name: Tat
- first_name: Noemi
full_name: Cannizzaro, Noemi
last_name: Cannizzaro
- first_name: Ralph
full_name: Green, Ralph
last_name: Green
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Konstantinos S.
full_name: Zarbalis, Konstantinos S.
last_name: Zarbalis
citation:
ama: Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position
and morphology of cortical neurons. Molecular Autism. 2022;13. doi:10.1186/s13229-022-00508-3
apa: Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer,
S., & Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology
of cortical neurons. Molecular Autism. Springer Nature. https://doi.org/10.1186/s13229-022-00508-3
chicago: Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke,
Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar
Position and Morphology of Cortical Neurons.” Molecular Autism. Springer
Nature, 2022. https://doi.org/10.1186/s13229-022-00508-3.
ieee: Z. A. Schaaf et al., “WDFY3 mutation alters laminar position and morphology
of cortical neurons,” Molecular Autism, vol. 13. Springer Nature, 2022.
ista: Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis
KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons.
Molecular Autism. 13, 27.
mla: Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology
of Cortical Neurons.” Molecular Autism, vol. 13, 27, Springer Nature, 2022,
doi:10.1186/s13229-022-00508-3.
short: Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer,
K.S. Zarbalis, Molecular Autism 13 (2022).
date_created: 2022-06-23T14:28:55Z
date_published: 2022-06-22T00:00:00Z
date_updated: 2023-08-03T07:21:32Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1186/s13229-022-00508-3
external_id:
isi:
- '000814641400001'
file:
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creator: dernst
date_created: 2022-06-24T08:22:59Z
date_updated: 2022-06-24T08:22:59Z
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file_name: 2022_MolecularAutism_Schaaf.pdf
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relation: main_file
success: 1
file_date_updated: 2022-06-24T08:22:59Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- Psychiatry and Mental health
- Developmental Biology
- Developmental Neuroscience
- Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Molecular Autism
publication_identifier:
issn:
- 2040-2392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1186/s13229-023-00539-4
status: public
title: WDFY3 mutation alters laminar position and morphology of cortical neurons
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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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...