---
_id: '9618'
abstract:
- lang: eng
text: The control of nonequilibrium quantum dynamics in many-body systems is challenging
because interactions typically lead to thermalization and a chaotic spreading
throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches
in a many-body system composed of 3 to 200 strongly interacting qubits in one
and two spatial dimensions. Using a programmable quantum simulator based on Rydberg
atom arrays, we show that coherent revivals associated with so-called quantum
many-body scars can be stabilized by periodic driving, which generates a robust
subharmonic response akin to discrete time-crystalline order. We map Hilbert space
dynamics, geometry dependence, phase diagrams, and system-size dependence of this
emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body
systems and enabling potential applications in quantum information science.
acknowledgement: 'We thank many members of the Harvard AMO community, particularly
E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive
operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado,
H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We
acknowledge financial support from the Center for Ultracold Atoms, the National
Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of
Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research,
the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033),
and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support
from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie
and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate
(NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center
for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science
Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s
EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and
the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute
for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K.,
G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed
the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed
theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors
discussed the results and contributed to the manuscript. Competing interests: M.G.,
V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a
shareholder of QuEra Computing. Data and materials availability: All data needed
to evaluate the conclusions in the paper are present in the paper and the supplementary
materials.'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Bluvstein, D.
last_name: Bluvstein
- first_name: A.
full_name: Omran, A.
last_name: Omran
- first_name: H.
full_name: Levine, H.
last_name: Levine
- first_name: A.
full_name: Keesling, A.
last_name: Keesling
- first_name: G.
full_name: Semeghini, G.
last_name: Semeghini
- first_name: S.
full_name: Ebadi, S.
last_name: Ebadi
- first_name: T. T.
full_name: Wang, T. T.
last_name: Wang
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: N.
full_name: Maskara, N.
last_name: Maskara
- first_name: W. W.
full_name: Ho, W. W.
last_name: Ho
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: M.
full_name: Greiner, M.
last_name: Greiner
- first_name: V.
full_name: Vuletić, V.
last_name: Vuletić
- first_name: M. D.
full_name: Lukin, M. D.
last_name: Lukin
citation:
ama: Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics
in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530
apa: Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S.,
… Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg
atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530
chicago: Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi,
T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom
Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.
ieee: D. Bluvstein et al., “Controlling quantum many-body dynamics in driven
Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359,
2021.
ista: Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT,
Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin
MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays.
Science. 371(6536), 1355–1359.
mla: Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg
Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530.
short: D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T.
Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V.
Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.
date_created: 2021-06-29T12:04:05Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2023-08-10T13:57:07Z
day: '26'
ddc:
- '539'
department:
- _id: MaSe
doi: 10.1126/science.abg2530
ec_funded: 1
external_id:
arxiv:
- '2012.12276'
isi:
- '000636043400048'
pmid:
- '33632894'
file:
- access_level: open_access
checksum: 0b356fd10ab9bb95177d4c047d4e9c1a
content_type: application/pdf
creator: patrickd
date_created: 2021-09-23T14:00:05Z
date_updated: 2021-09-23T14:00:05Z
file_id: '10040'
file_name: scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf
file_size: 3671159
relation: main_file
success: 1
file_date_updated: 2021-09-23T14:00:05Z
has_accepted_license: '1'
intvolume: ' 371'
isi: 1
issue: '6536'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
page: 1355-1359
pmid: 1
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Controlling quantum many-body dynamics in driven Rydberg atom arrays
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 371
year: '2021'
...
---
_id: '9657'
abstract:
- lang: eng
text: To overcome nitrogen deficiency, legume roots establish symbiotic interactions
with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules).
Similar to other organs, nodule formation is determined by a local maximum of
the phytohormone auxin at the primordium site. However, how auxin regulates nodule
development remains poorly understood. Here, we found that in soybean, (Glycine
max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is
involved in nodule primordium formation. GmPIN1 was specifically expressed in
nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation
regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical
cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated
with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems
and aberrant divisions in the nodule primordium cells. Moreover, overexpression
of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis
thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally
transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement.
Our findings reveal how PIN-dependent auxin transport modulates different aspects
of soybean nodule development and suggest that establishment of auxin gradient
is a prerequisite for the proper interaction between legumes and rhizobia.
article_processing_charge: No
article_type: original
author:
- first_name: Z
full_name: Gao, Z
last_name: Gao
- first_name: Z
full_name: Chen, Z
last_name: Chen
- first_name: Y
full_name: Cui, Y
last_name: Cui
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: H
full_name: Xu, H
last_name: Xu
- first_name: Q
full_name: Xu, Q
last_name: Xu
- first_name: J
full_name: Chen, J
last_name: Chen
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: L
full_name: Huang, L
last_name: Huang
- first_name: H
full_name: Zhao, H
last_name: Zhao
- first_name: D
full_name: Huang, D
last_name: Huang
- first_name: S
full_name: Mai, S
last_name: Mai
- first_name: T
full_name: Xu, T
last_name: Xu
- first_name: X
full_name: Liu, X
last_name: Liu
- first_name: S
full_name: Li, S
last_name: Li
- first_name: Y
full_name: Guan, Y
last_name: Guan
- first_name: W
full_name: Yang, W
last_name: Yang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Petrášek, J
last_name: Petrášek
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: X
full_name: Chen, X
last_name: Chen
citation:
ama: Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved
in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183
apa: Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent
polar auxin transport is involved in soybean nodule development. Plant Cell.
American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183
chicago: Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent
Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell.
American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.
ieee: Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in
soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society
of Plant Biologists, pp. 2981–3003, 2021.
ista: Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang
D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen
X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development.
Plant Cell. 33(9), 2981–3003.
mla: Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean
Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant
Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.
short: Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H.
Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek,
J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.
date_created: 2021-07-14T15:32:43Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-10T14:01:41Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plcell/koab183
external_id:
isi:
- '000702165300012'
pmid:
- '34240197'
file:
- access_level: open_access
checksum: 6715712ec306c321f0204c817b7f8ae7
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T12:13:34Z
date_updated: 2021-07-19T12:13:34Z
file_id: '9691'
file_name: 2021_PlantCell_Gao.pdf
file_size: 10566921
relation: main_file
success: 1
file_date_updated: 2021-07-19T12:13:34Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '9'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2981–3003
pmid: 1
publication: Plant Cell
publication_identifier:
eissn:
- 1532-298x
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: GmPIN-dependent polar auxin transport is involved in soybean nodule development
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2021'
...
---
_id: '9640'
abstract:
- lang: eng
text: 'Selection and random drift determine the probability that novel mutations
fixate in a population. Population structure is known to affect the dynamics of
the evolutionary process. Amplifiers of selection are population structures that
increase the fixation probability of beneficial mutants compared to well-mixed
populations. Over the past 15 years, extensive research has produced remarkable
structures called strong amplifiers which guarantee that every beneficial mutation
fixates with high probability. But strong amplification has come at the cost of
considerably delaying the fixation event, which can slow down the overall rate
of evolution. However, the precise relationship between fixation probability and
time has remained elusive. Here we characterize the slowdown effect of strong
amplification. First, we prove that all strong amplifiers must delay the fixation
event at least to some extent. Second, we construct strong amplifiers that delay
the fixation event only marginally as compared to the well-mixed populations.
Our results thus establish a tight relationship between fixation probability and
time: Strong amplification always comes at a cost of a slowdown, but more than
a marginal slowdown is not needed.'
acknowledgement: 'K.C. acknowledges support from ERC Start grant no. (279307: Graph
Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF)
grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office
of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.'
article_number: '4009'
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers
of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w
apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast
and strong amplifiers of natural selection. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-24271-w
chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin
A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.
ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong
amplifiers of natural selection,” Nature Communications, vol. 12, no. 1.
Springer Nature, 2021.
ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers
of natural selection. Nature Communications. 12(1), 4009.
mla: Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature
Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.
short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications
12 (2021).
date_created: 2021-07-11T22:01:15Z
date_published: 2021-06-29T00:00:00Z
date_updated: 2023-08-10T14:05:09Z
day: '29'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1038/s41467-021-24271-w
ec_funded: 1
external_id:
isi:
- '000671752100003'
pmid:
- '34188036'
file:
- access_level: open_access
checksum: 5767418926a7f7fb76151de29473dae0
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:02:20Z
date_updated: 2021-07-19T13:02:20Z
file_id: '9692'
file_name: 2021_NatCoom_Tkadlec.pdf
file_size: 628992
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:02:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and strong amplifiers of natural selection
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: 12
year: '2021'
...
---
_id: '9656'
abstract:
- lang: eng
text: Tropisms, growth responses to environmental stimuli such as light or gravity,
are spectacular examples of adaptive plant development. The plant hormone auxin
serves as a major coordinative signal. The PIN auxin exporters, through their
dynamic polar subcellular localizations, redirect auxin fluxes in response to
environmental stimuli and the resulting auxin gradients across organs underly
differential cell elongation and bending. In this review, we discuss recent advances
concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation
and trafficking. We also cover how environmental cues regulate PIN actions during
tropisms, and a crucial role of auxin feedback on PIN polarity during bending
termination. Finally, the interactions between different tropisms are reviewed
to understand plant adaptive growth in the natural environment.
acknowledgement: We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and
Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript.
We apologize to those researchers whose great work was not cited. This work is supported
by the European Research Council under the European Union’s Horizon 2020 research
and innovation Programme (ERC grant agreement number 742985), and the Austrian Science
Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship
Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture
University (9232308314).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport
regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522.
doi:10.1111/nph.17617
apa: Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated
polar auxin transport regulations in plant tropic responses. New Phytologist.
Wiley. https://doi.org/10.1111/nph.17617
chicago: Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml.
“PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New
Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.
ieee: H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar
auxin transport regulations in plant tropic responses,” New Phytologist,
vol. 232, no. 2. Wiley, pp. 510–522, 2021.
ista: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin
transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.
mla: Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant
Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22,
doi:10.1111/nph.17617.
short: H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021)
510–522.
date_created: 2021-07-14T15:29:14Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-08-10T14:02:41Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.17617
ec_funded: 1
external_id:
isi:
- '000680587100001'
pmid:
- '34254313'
file:
- access_level: open_access
checksum: 6422a6eb329b52d96279daaee0fcf189
content_type: application/pdf
creator: kschuh
date_created: 2021-10-07T13:42:47Z
date_updated: 2021-10-07T13:42:47Z
file_id: '10105'
file_name: 2021_NewPhytologist_Han.pdf
file_size: 1939800
relation: main_file
success: 1
file_date_updated: 2021-10-07T13:42:47Z
has_accepted_license: '1'
intvolume: ' 232'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 510-522
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-mediated polar auxin transport regulations in plant tropic responses
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: 232
year: '2021'
...
---
_id: '9679'
abstract:
- lang: eng
text: The relative motion of three impenetrable particles on a ring, in our case
two identical fermions and one impurity, is isomorphic to a triangular quantum
billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards
can be integrable or non-integrable (also referred to in the main text as chaotic).
To set the stage, we first investigate the energy level distributions of the billiards
as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond
the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to
analyze properties of probability distributions of individual quantum states.
We find that convolutional neural networks can correctly classify integrable and
non-integrable states. The decisive features of the wave functions are the normalization
and a large number of zero elements, corresponding to the existence of a nodal
line. The network achieves typical accuracies of 97%, suggesting that machine
learning tools can be used to analyze and classify the morphology of probability
densities obtained in theory or experiment.
acknowledgement: We thank Aidan Tracy for his input during the initial stages of this
project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane
Hudson Smith for helpful discussions and comments on the manuscript. This work has
been supported by European Union's Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German
Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by
the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248)
(AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research
Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung
und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality
during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to
Quarks'. This infrastructure is part of a project that has received funding from
the European Union's Horizon 2020 research and innovation program under Grant Agreement
No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the
Open Access Publishing Fund of Technische Universität Darmstadt.
article_number: '065009'
article_processing_charge: Yes
article_type: original
author:
- first_name: David
full_name: Huber, David
last_name: Huber
- first_name: Oleksandr V.
full_name: Marchukov, Oleksandr V.
last_name: Marchukov
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum
states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576
apa: Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology
of three-body quantum states from machine learning. New Journal of Physics.
IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576
chicago: Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev.
“Morphology of Three-Body Quantum States from Machine Learning.” New Journal
of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576.
ieee: D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of
three-body quantum states from machine learning,” New Journal of Physics,
vol. 23, no. 6. IOP Publishing, 2021.
ista: Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body
quantum states from machine learning. New Journal of Physics. 23(6), 065009.
mla: Huber, David, et al. “Morphology of Three-Body Quantum States from Machine
Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing,
2021, doi:10.1088/1367-2630/ac0576.
short: D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics
23 (2021).
date_created: 2021-07-18T22:01:22Z
date_published: 2021-06-23T00:00:00Z
date_updated: 2023-08-10T13:58:09Z
day: '23'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/ac0576
ec_funded: 1
external_id:
arxiv:
- '2102.04961'
isi:
- '000664736300001'
file:
- access_level: open_access
checksum: e39164ce7ea228d287cf8924e1a0f9fe
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T11:47:16Z
date_updated: 2021-07-19T11:47:16Z
file_id: '9690'
file_name: 2021_NewJPhys_Huber.pdf
file_size: 3868445
relation: main_file
success: 1
file_date_updated: 2021-07-19T11:47:16Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: New Journal of Physics
publication_identifier:
eissn:
- '13672630'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology of three-body quantum states from machine 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...
---
_id: '9629'
abstract:
- lang: eng
text: Intestinal organoids derived from single cells undergo complex crypt–villus
patterning and morphogenesis. However, the nature and coordination of the underlying
forces remains poorly characterized. Here, using light-sheet microscopy and large-scale
imaging quantification, we demonstrate that crypt formation coincides with a stark
reduction in lumen volume. We develop a 3D biophysical model to computationally
screen different mechanical scenarios of crypt morphogenesis. Combining this with
live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven
crypt apical contraction and villus basal tension work synergistically with lumen
volume reduction to drive crypt morphogenesis, and demonstrate the existence of
a critical point in differential tensions above which crypt morphology becomes
robust to volume changes. Finally, we identified a sodium/glucose cotransporter
that is specific to differentiated enterocytes that modulates lumen volume reduction
through cell swelling in the villus region. Together, our study uncovers the cellular
basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust
morphogenesis.
acknowledgement: 'We acknowledge the members of the Lennon-Duménil laboratory for
sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali
laboratory and the FMI facilities for their support. We thank E. Tagliavini for
IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for
helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell
sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler
for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members
of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing
feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from
Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European
Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme
Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531,
to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program
Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to
E.H.).'
article_processing_charge: No
article_type: original
author:
- first_name: Qiutan
full_name: Yang, Qiutan
last_name: Yang
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Chii Jou
full_name: Chan, Chii Jou
last_name: Chan
- first_name: Markus
full_name: Rempfler, Markus
last_name: Rempfler
- first_name: Dario
full_name: Vischi, Dario
last_name: Vischi
- first_name: Francisca
full_name: Maurer-Gutierrez, Francisca
last_name: Maurer-Gutierrez
- first_name: Takashi
full_name: Hiiragi, Takashi
last_name: Hiiragi
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Prisca
full_name: Liberali, Prisca
last_name: Liberali
citation:
ama: Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces
in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2
apa: Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez,
F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal
crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2
chicago: Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi,
Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali.
“Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.”
Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.
ieee: Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal
crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744,
2021.
ista: Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi
T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces
in intestinal crypt formation. Nature Cell Biology. 23, 733–744.
mla: Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal
Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021,
pp. 733–744, doi:10.1038/s41556-021-00700-2.
short: Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez,
T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.
date_created: 2021-07-04T22:01:25Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-08-10T13:57:36Z
day: '21'
department:
- _id: EdHa
doi: 10.1038/s41556-021-00700-2
ec_funded: 1
external_id:
isi:
- '000664016300003'
pmid:
- '34155381'
intvolume: ' 23'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.05.13.094359
month: '06'
oa: 1
oa_version: Preprint
page: 733–744
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell fate coordinates mechano-osmotic forces in intestinal crypt formation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...
---
_id: '9626'
abstract:
- lang: eng
text: SnSe, a wide-bandgap semiconductor, has attracted significant attention from
the thermoelectric (TE) community due to its outstanding TE performance deriving
from the ultralow thermal conductivity and advantageous electronic structures.
Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap
engineering and vacancy compensation. We found that PbTe can significantly reduce
the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing
the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases
the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum
ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found
that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and
form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain
boundary could also reduce the intergrain energy barrier which largely enhances
the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an
average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe.
Our findings provide a novel strategy to promote the TE performance in wide-bandgap
semiconductors.
acknowledgement: This work was supported by National Natural Science Foundation of
China (51772012), National Key Research and Development Program of China (2018YFA0702100
and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work
was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral
Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the
High Performance Computing (HPC) resources at Beihang University, the National Science
Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science
and Technology Advanced Research (HPSTAR) for SEM measurements.
article_number: '100452'
article_processing_charge: No
article_type: original
author:
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Tao
full_name: Hong, Tao
last_name: Hong
- first_name: Dongyang
full_name: Wang, Dongyang
last_name: Wang
- first_name: Sining
full_name: Wang, Sining
last_name: Wang
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Mengmeng
full_name: Zhang, Mengmeng
last_name: Zhang
- first_name: Xiang
full_name: Gao, Xiang
last_name: Gao
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric
performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation.
Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452
apa: Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021).
Realizing high doping efficiency and thermoelectric performance in n-type SnSe
polycrystals via bandgap engineering and vacancy compensation. Materials Today
Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452
chicago: Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng
Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency
and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering
and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452.
ieee: L. Su et al., “Realizing high doping efficiency and thermoelectric
performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,”
Materials Today Physics, vol. 20. Elsevier, 2021.
ista: Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021.
Realizing high doping efficiency and thermoelectric performance in n-type SnSe
polycrystals via bandgap engineering and vacancy compensation. Materials Today
Physics. 20, 100452.
mla: Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance
in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.”
Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452.
short: L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D.
Zhao, Materials Today Physics 20 (2021).
date_created: 2021-07-04T22:01:24Z
date_published: 2021-06-03T00:00:00Z
date_updated: 2023-08-10T13:56:31Z
day: '03'
department:
- _id: MaIb
doi: 10.1016/j.mtphys.2021.100452
external_id:
isi:
- '000703159600010'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
publication: Materials Today Physics
publication_identifier:
eissn:
- 2542-5293
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Realizing high doping efficiency and thermoelectric performance in n-type SnSe
polycrystals via bandgap engineering and vacancy compensation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2021'
...
---
_id: '9778'
abstract:
- lang: eng
text: The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit.
Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this
synaptic connection. It is widely believed that mossy fiber PTP is an entirely
presynaptic phenomenon, implying that PTP induction is input-specific, and requires
neither activity of multiple inputs nor stimulation of postsynaptic neurons. To
directly test cooperativity and associativity, we made paired recordings between
single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain
slices. By stimulating non-overlapping mossy fiber inputs converging onto single
CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly,
mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only
minimal PTP after combined pre- and postsynaptic high-frequency stimulation with
intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic
spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP
is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels,
group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde
vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire
of synaptic computations, implementing a brake on mossy fiber detonation and a
“smart teacher” function of hippocampal mossy fiber synapses.
acknowledged_ssus:
- _id: SSU
acknowledgement: We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically
reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois
Schlögl for help with analysis, Florian Marr for excellent technical assistance
and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller
for manuscript editing, and the Scientific Service Units of IST Austria for support.
This project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement No
692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27,
Wittgenstein award), both to P.J.
article_number: '2912'
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Yuji
full_name: Okamoto, Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term
plasticity in hippocampal mossy fiber synapses. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-23153-5
apa: Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation
of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature
Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5
chicago: Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation
of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature
Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5.
ieee: D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic
short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications,
vol. 12, no. 1. Springer, 2021.
ista: Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic
short-term plasticity in hippocampal mossy fiber synapses. Nature Communications.
12(1), 2912.
mla: Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term
Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications,
vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5.
short: D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).
date_created: 2021-08-06T07:22:55Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2023-08-10T14:16:16Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-021-23153-5
ec_funded: 1
external_id:
isi:
- '000655481800014'
file:
- access_level: open_access
checksum: 6036a8cdae95e1707c2a04d54e325ff4
content_type: application/pdf
creator: kschuh
date_created: 2021-12-17T11:34:50Z
date_updated: 2021-12-17T11:34:50Z
file_id: '10563'
file_name: 2021_NatureCommunications_Vandael.pdf
file_size: 3108845
relation: main_file
success: 1
file_date_updated: 2021-12-17T11:34:50Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/
scopus_import: '1'
status: public
title: Transsynaptic modulation of presynaptic short-term plasticity in hippocampal
mossy fiber synapses
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: 12
year: '2021'
...
---
_id: '9647'
abstract:
- lang: eng
text: 'Gene expression is regulated by the set of transcription factors (TFs) that
bind to the promoter. The ensuing regulating function is often represented as
a combinational logic circuit, where output (gene expression) is determined by
current input values (promoter bound TFs) only. However, the simultaneous arrival
of TFs is a strong assumption, since transcription and translation of genes introduce
intrinsic time delays and there is no global synchronisation among the arrival
times of different molecular species at their targets. We present an experimentally
implementable genetic circuit with two inputs and one output, which in the presence
of small delays in input arrival, exhibits qualitatively distinct population-level
phenotypes, over timescales that are longer than typical cell doubling times.
From a dynamical systems point of view, these phenotypes represent long-lived
transients: although they converge to the same value eventually, they do so after
a very long time span. The key feature of this toy model genetic circuit is that,
despite having only two inputs and one output, it is regulated by twenty-three
distinct DNA-TF configurations, two of which are more stable than others (DNA
looped states), one promoting and another blocking the expression of the output
gene. Small delays in input arrival time result in a majority of cells in the
population quickly reaching the stable state associated with the first input,
while exiting of this stable state occurs at a slow timescale. In order to mechanistically
model the behaviour of this genetic circuit, we used a rule-based modelling language,
and implemented a grid-search to find parameter combinations giving rise to long-lived
transients. Our analysis shows that in the absence of feedback, there exist path-dependent
gene regulatory mechanisms based on the long timescale of transients. The behaviour
of this toy model circuit suggests that gene regulatory networks can exploit event
timing to create phenotypes, and it opens the possibility that they could use
event timing to memorise events, without regulatory feedback. The model reveals
the importance of (i) mechanistically modelling the transitions between the different
DNA-TF states, and (ii) employing transient analysis thereof.'
acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced
Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science,
Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence
2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia
Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences.
Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).'
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Petrov, Tatjana
last_name: Petrov
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in
gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023
apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021).
Long lived transients in gene regulation. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023
chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin
C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.
ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived
transients in gene regulation,” Theoretical Computer Science, vol. 893.
Elsevier, pp. 1–16, 2021.
ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients
in gene regulation. Theoretical Computer Science. 893, 1–16.
mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical
Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.
short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer
Science 893 (2021) 1–16.
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2023-08-10T14:11:19Z
day: '04'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1016/j.tcs.2021.05.023
external_id:
isi:
- '000710180500002'
file:
- access_level: open_access
checksum: d3aef34cfb13e53bba4cf44d01680793
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:13:27Z
date_updated: 2022-05-12T12:13:27Z
file_id: '11364'
file_name: 2021_TheoreticalComputerScience_Petrov.pdf
file_size: 2566504
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:13:27Z
has_accepted_license: '1'
intvolume: ' 893'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-16
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long lived transients in gene regulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 893
year: '2021'
...
---
_id: '9761'
abstract:
- lang: eng
text: 'The important roles of mitochondrial function and dysfunction in the process
of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear
to be a highly vulnerable neuronal cell type in the central nervous system with
respect to mitochondrial dysfunction but the actual reasons for this are still
incompletely understood. These cells have a unique circumstance where unmyelinated
axons must bend nearly 90° to exit the eye and then cross a translaminar pressure
gradient before becoming myelinated in the optic nerve. This region, the optic
nerve head, contains some of the highest density of mitochondria present in these
cells. Glaucoma represents a perfect storm of events occurring at this location,
with a combination of changes in the translaminar pressure gradient and reassignment
of the metabolic support functions of supporting glia, which appears to apply
increased metabolic stress to the RGC axons leading to a failure of axonal transport
mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations,
particularly in genes affecting mitochondrial dynamics and mitochondrial clearance.
These mutations, which systemically affect the mitochondria in every cell, often
lead to an optic neuropathy as the sole pathologic defect in affected patients.
This review summarizes knowledge of mitochondrial structure and function, the
known energy demands of neurons in general, and places these in the context of
normal and pathological characteristics of mitochondria attributed to RGCs. '
acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for
generously sharing some of their data for this review, and to Janis Eells for helpful
comments on the manuscript.
article_number: '1593'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole A.
full_name: Muench, Nicole A.
last_name: Muench
- first_name: Sonia
full_name: Patel, Sonia
last_name: Patel
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Akihiro
full_name: Ikeda, Akihiro
last_name: Ikeda
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593
apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells,
R. W. (2021). The influence of mitochondrial dynamics and function on retinal
ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593
chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro
Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071593.
ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells,
“The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.
ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 10(7), 1593.
mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells,
vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.
short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells,
Cells 10 (2021).
date_created: 2021-08-01T22:01:22Z
date_published: 2021-06-25T00:00:00Z
date_updated: 2023-08-10T14:14:53Z
day: '25'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.3390/cells10071593
external_id:
isi:
- '000678193300001'
pmid:
- '34201955'
file:
- access_level: open_access
checksum: e0497ce5c77fa3b65a538c7d6e0f6c66
content_type: application/pdf
creator: cziletti
date_created: 2021-08-04T14:01:30Z
date_updated: 2021-08-04T14:01:30Z
file_id: '9768'
file_name: 2021_Cells_Muench.pdf
file_size: 4555611
relation: main_file
success: 1
file_date_updated: 2021-08-04T14:01:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
eissn:
- '20734409'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease
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: 10
year: '2021'
...
---
_id: '9641'
abstract:
- lang: eng
text: At the encounter with a novel environment, contextual memory formation is
greatly enhanced, accompanied with increased arousal and active exploration. Although
this phenomenon has been widely observed in animal and human daily life, how the
novelty in the environment is detected and contributes to contextual memory formation
has lately started to be unveiled. The hippocampus has been studied for many decades
for its largely known roles in encoding spatial memory, and a growing body of
evidence indicates a differential involvement of dorsal and ventral hippocampal
divisions in novelty detection. In this brief review article, we discuss the recent
findings of the role of mossy cells in the ventral hippocampal moiety in novelty
detection and put them in perspective with other novelty-related pathways in the
hippocampus. We propose a mechanism for novelty-driven memory acquisition in the
dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate
granule cells. By this projection, the ventral hippocampus sends novelty signals
to the dorsal hippocampus, opening a gate for memory encoding in dentate granule
cells based on information coming from the entorhinal cortex. We conclude that,
contrary to the presently accepted functional independence, the dorsal and ventral
hippocampi cooperate to link the novelty and contextual information, and this
dorso-ventral interaction is crucial for the novelty-dependent memory formation.
acknowledgement: This work was supported by a European Research Council Advanced Grant
694539 to Ryuichi Shigemoto.
article_number: '107486'
article_processing_charge: No
article_type: original
author:
- first_name: Felipe
full_name: Fredes, Felipe
last_name: Fredes
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection.
Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486
apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells
in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486
chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021.
https://doi.org/10.1016/j.nlm.2021.107486.
ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty
detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.
ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty
detection. Neurobiology of Learning and Memory. 183, 107486.
mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486,
Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.
short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-06-30T00:00:00Z
date_updated: 2023-08-10T14:10:37Z
day: '30'
ddc:
- '610'
department:
- _id: RySh
doi: 10.1016/j.nlm.2021.107486
ec_funded: 1
external_id:
isi:
- '000677694900004'
pmid:
- '34214666'
file:
- access_level: open_access
checksum: 8e8298a9e8c7df146ad23f32c2a63929
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:46:06Z
date_updated: 2021-07-19T13:46:06Z
file_id: '9694'
file_name: 2021_NeurobLearnMemory_Fredes.pdf
file_size: 1994793
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:46:06Z
has_accepted_license: '1'
intvolume: ' 183'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Neurobiology of Learning and Memory
publication_identifier:
eissn:
- '10959564'
issn:
- '10747427'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of hippocampal mossy cells in novelty detection
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 183
year: '2021'
...
---
_id: '9646'
abstract:
- lang: eng
text: We consider the fundamental problem of deriving quantitative bounds on the
probability that a given assertion is violated in a probabilistic program. We
provide automated algorithms that obtain both lower and upper bounds on the assertion
violation probability. The main novelty of our approach is that we prove new and
dedicated fixed-point theorems which serve as the theoretical basis of our algorithms
and enable us to reason about assertion violation bounds in terms of pre and post
fixed-point functions. To synthesize such fixed-points, we devise algorithms that
utilize a wide range of mathematical tools, including repulsing ranking supermartingales,
Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization.
On the theoretical side, we provide (i) the first automated algorithm for lower-bounds
on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds
of exponential form in affine programs, and (iii) provably and significantly tighter
upper-bounds than the previous approaches. On the practical side, we show our
algorithms can handle a wide variety of programs from the literature and synthesize
bounds that are remarkably tighter than previous results, in some cases by thousands
of orders of magnitude.
acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful
and valuable comments. The work was partially supported by the National Natural
Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research
Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and
DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).'
article_processing_charge: No
author:
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of
assertion violations in probabilistic programs. In: Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102'
apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021).
Quantitative analysis of assertion violations in probabilistic programs. In Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 1171–1186). Online: Association for Computing Machinery.
https://doi.org/10.1145/3453483.3454102'
chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.”
In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 1171–86. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454102.
ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative
analysis of assertion violations in probabilistic programs,” in Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Online, 2021, pp. 1171–1186.
ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis
of assertion violations in probabilistic programs. Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 1171–1186.'
mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic
Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on
Programming Language Design and Implementation, Association for Computing
Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.
short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:14:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454102
ec_funded: 1
external_id:
arxiv:
- '2011.14617'
isi:
- '000723661700076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.14617
month: '06'
oa: 1
oa_version: Preprint
page: 1171-1186
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative analysis of assertion violations in probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9645'
abstract:
- lang: eng
text: "We consider the fundamental problem of reachability analysis over imperative
programs with real variables. Previous works that tackle reachability are either
unable to handle programs consisting of general loops (e.g. symbolic execution),
or lack completeness guarantees (e.g. abstract interpretation), or are not automated
(e.g. incorrectness logic). In contrast, we propose a novel approach for reachability
analysis that can handle general and complex loops, is complete, and can be entirely
automated for a wide family of programs. Through the notion of Inductive Reachability
Witnesses (IRWs), our approach extends ideas from both invariant generation and
termination to reachability analysis.\r\n\r\nWe first show that our IRW-based
approach is sound and complete for reachability analysis of imperative programs.
Then, we focus on linear and polynomial programs and develop automated methods
for synthesizing linear and polynomial IRWs. In the linear case, we follow the
well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial
case, where we present a push-button semi-complete algorithm. We achieve this
using a novel combination of classical theorems in real algebraic geometry, such
as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally,
our experimental results show we can prove complex reachability objectives over
various benchmarks that were beyond the reach of previous methods."
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the
Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC
Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Mohammad
full_name: Mahdavi, Mohammad
last_name: Mahdavi
citation:
ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability
witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076'
apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021).
Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076'
chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady,
and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 772–87. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454076.
ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial
reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN
International Conference on Programming Language Design and Implementation,
Online, 2021, pp. 772–787.
ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability
witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 772–787.'
mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–87,
doi:10.1145/3453483.3454076.
short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–787.
conference:
end_date: 2021-06-26
location: Online
name: ' PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:13:39Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454076
ec_funded: 1
external_id:
isi:
- '000723661700050'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03183862/
month: '06'
oa: 1
oa_version: Submitted Version
page: 772-787
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polynomial reachability witnesses via Stellensätze
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9759'
acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable
comments on an earlier version of the manuscript. We also thank the facilitators
of the 2019–2020 eLife Community Ambassador program.
article_number: e1009124
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Michael John
full_name: Bartlett, Michael John
last_name: Bartlett
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Adriana
full_name: Bankston, Adriana
last_name: Bankston
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
citation:
ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve
academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124
apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021).
Ten simple rules to improve academic work- life balance. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124
chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz
Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS
Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.
ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple
rules to improve academic work- life balance,” PLoS Computational Biology,
vol. 17, no. 7. Public Library of Science, 2021.
ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to
improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.
mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work-
Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public
Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.
short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational
Biology 17 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-08-10T14:16:46Z
day: '15'
ddc:
- '613'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1009124
external_id:
isi:
- '000677713500008'
pmid:
- '34264932'
file:
- access_level: open_access
checksum: e56d91f0eeadb36f143a90e2c1b3ab63
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-05T12:06:49Z
date_updated: 2021-08-05T12:06:49Z
file_id: '9771'
file_name: 2021_PlosCompBio_Bartlett.pdf
file_size: 693633
relation: main_file
file_date_updated: 2021-08-05T12:06:49Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
scopus_import: '1'
status: public
title: Ten simple rules to improve academic work- life balance
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: 17
year: '2021'
...
---
_id: '9822'
abstract:
- lang: eng
text: Attachment of adhesive molecules on cell culture surfaces to restrict cell
adhesion to defined areas and shapes has been vital for the progress of in vitro
research. In currently existing patterning methods, a combination of pattern properties
such as stability, precision, specificity, high-throughput outcome, and spatiotemporal
control is highly desirable but challenging to achieve. Here, we introduce a versatile
and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent
patterning step and a subsequent functionalization of the pattern via click chemistry.
This two-step process is feasible on arbitrary surfaces and allows for generation
of sustainable patterns and gradients. The method is validated in different biological
systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining
the growth and migration of cells to the designated areas. We then implement a
sequential photopatterning approach by adding a second switchable patterning step,
allowing for spatiotemporal control over two distinct surface patterns. As a proof
of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis.
Our results show that the spatiotemporal control provided by our “sequential photopatterning”
system is essential for mimicking dynamic biological processes and that our innovative
approach has great potential for further applications in cell science.
acknowledgement: We would like to thank Charlott Leu for the production of our chromium
wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh
Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim
Rädler for his valuable scientific guidance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Miriam
full_name: Balles, Miriam
last_name: Balles
- first_name: Maibritt
full_name: Kretschmer, Maibritt
last_name: Kretschmer
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Janina
full_name: Lange, Janina
last_name: Lange
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for
studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R.
P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular
processes under spatiotemporal control. ACS Applied Materials and Interfaces.
American Chemical Society. https://doi.org/10.1021/acsami.1c09850
chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria
Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning
for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied
Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
ieee: T. Zisis et al., “Sequential and switchable patterning for studying
cellular processes under spatiotemporal control,” ACS Applied Materials and
Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.
ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild
R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning
for studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 13(30), 35545–35560.
mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying
Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and
Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560,
doi:10.1021/acsami.1c09850.
short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait,
R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials
and Interfaces 13 (2021) 35545–35560.
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-10T14:22:48Z
day: '04'
ddc:
- '620'
- '570'
department:
- _id: MiSi
- _id: GaTk
- _id: Bio
- _id: CaGu
doi: 10.1021/acsami.1c09850
ec_funded: 1
external_id:
isi:
- '000683741400026'
pmid:
- '34283577'
file:
- access_level: open_access
checksum: b043a91d9f9200e467b970b692687ed3
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:44:03Z
date_updated: 2021-08-09T09:44:03Z
file_id: '9833'
file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf
file_size: 7123293
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:44:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '30'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 35545–35560
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential and switchable patterning for studying cellular processes under
spatiotemporal control
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2021'
...
---
_id: '9819'
abstract:
- lang: eng
text: Photorealistic editing of head portraits is a challenging task as humans are
very sensitive to inconsistencies in faces. We present an approach for high-quality
intuitive editing of the camera viewpoint and scene illumination (parameterised
with an environment map) in a portrait image. This requires our method to capture
and control the full reflectance field of the person in the image. Most editing
approaches rely on supervised learning using training data captured with setups
such as light and camera stages. Such datasets are expensive to acquire, not readily
available and do not capture all the rich variations of in-the-wild portrait images.
In addition, most supervised approaches only focus on relighting, and do not allow
camera viewpoint editing. Thus, they only capture and control a subset of the
reflectance field. Recently, portrait editing has been demonstrated by operating
in the generative model space of StyleGAN. While such approaches do not require
direct supervision, there is a significant loss of quality when compared to the
supervised approaches. In this paper, we present a method which learns from limited
supervised training data. The training images only include people in a fixed neutral
expression with eyes closed, without much hair or background variations. Each
person is captured under 150 one-light-at-a-time conditions and under 8 camera
poses. Instead of training directly in the image space, we design a supervised
problem which learns transformations in the latent space of StyleGAN. This combines
the best of supervised learning and generative adversarial modeling. We show that
the StyleGAN prior allows for generalisation to different expressions, hairstyles
and backgrounds. This produces high-quality photorealistic results for in-the-wild
images and significantly outperforms existing methods. Our approach can edit the
illumination and pose simultaneously, and runs at interactive rates.
acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784).
We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng
Sun for kindly helping us with the comparisons with Sun et al. [2019].
article_number: '44'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Abdallah
full_name: Dib, Abdallah
last_name: Dib
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Louis
full_name: Chevallier, Louis
last_name: Chevallier
- first_name: Mohamed A.
full_name: Elgharib, Mohamed A.
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance
editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765'
apa: 'Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel,
H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head
portraits. ACM Transactions on Graphics. Association for Computing Machinery.
https://doi.org/10.1145/3450626.3459765'
chicago: 'Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel,
Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance
Editing of Head Portraits.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.'
ieee: 'B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing
of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association
for Computing Machinery, 2021.'
ista: 'Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister
H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic
appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.'
mla: 'Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of
Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association
for Computing Machinery, 2021, doi:10.1145/3450626.3459765.'
short: B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel,
H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:25:08Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3450626.3459765
external_id:
arxiv:
- '2103.07658'
isi:
- '000674930900011'
file:
- access_level: open_access
checksum: 51b61b7e5c175e2d7ed8fa3b35f7525a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:41:50Z
date_updated: 2021-08-09T11:41:50Z
file_id: '9834'
file_name: 2021_ACMTransactionsOnGraphics_Mallikarjun.pdf
file_size: 49840741
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:41:50Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PhotoApp: Photorealistic appearance editing of head portraits'
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: 40
year: '2021'
...
---
_id: '9816'
abstract:
- lang: eng
text: "Aims: Mass antigen testing programs have been challenged because of an alleged
insufficient specificity, leading to a large number of false positives. The objective
of this study is to derive a lower bound of the specificity of the SD Biosensor
Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data
from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020
we calculate a lower confidence bound for the specificity. As positive test results
were not systematically verified by PCR tests, we base the lower bound on a worst
case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332
persons from 79 counties were tested. The lowest positivity rate was observed
in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This
implies a test specificity of at least 99.6% (97.5% one-sided lower confidence
bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests
a higher specificity compared to earlier studies in spite of the underlying worst
case assumption and the application in a mass testing setting. The actual specificity
is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible
at the time of testing. To our knowledge, this estimate constitutes the first
bound obtained from large scale practical use of an antigen test."
acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová
for very helpful comments. We also thank Matej Mišík for discussion and information
regarding the Slovak testing data and Ag-Test used.
article_number: e0255267
article_processing_charge: Yes
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Mathias
full_name: Beiglböck, Mathias
last_name: Beiglböck
- first_name: Anna Nele
full_name: Herdina, Anna Nele
last_name: Herdina
- first_name: Robert
full_name: Strassl, Robert
last_name: Strassl
- first_name: Martin
full_name: Posch, Martin
last_name: Posch
citation:
ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis
of the specificity of a COVID-19 antigen test in the Slovak mass testing program.
PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267
apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &
Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the
Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267
chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina,
Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen
Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0255267.
ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch,
“Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021.
Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program. PLoS ONE. 16(7), e0255267.
mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test
in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267,
Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.
short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2023-08-10T14:26:32Z
day: '29'
ddc:
- '610'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0255267
external_id:
isi:
- '000685248200095'
pmid:
- '34324553'
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creator: asandaue
date_created: 2021-08-09T11:52:14Z
date_updated: 2021-08-09T11:52:14Z
file_id: '9835'
file_name: 2021_PLoSONE_Hledík.pdf
file_size: 773921
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:52:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program
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: 16
year: '2021'
...
---
_id: '9821'
abstract:
- lang: eng
text: Heart rate variability (hrv) is a physiological phenomenon of the variation
in the length of the time interval between consecutive heartbeats. In many cases
it could be an indicator of the development of pathological states. The classical
approach to the analysis of hrv includes time domain methods and frequency domain
methods. However, attempts are still being made to define new and more effective
hrv assessment tools. Persistent homology is a novel data analysis tool developed
in the recent decades that is rooted at algebraic topology. The Topological Data
Analysis (TDA) approach focuses on examining the shape of the data in terms of
connectedness and holes, and has recently proved to be very effective in various
fields of research. In this paper we propose the use of persistent homology to
the hrv analysis. We recall selected topological descriptors used in the literature
and we introduce some new topological descriptors that reflect the specificity
of hrv, and we discuss their relation to the standard hrv measures. In particular,
we show that this novel approach provides a collection of indices that might be
at least as useful as the classical parameters in differentiating between series
of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering
from a stroke episode.
acknowledgement: We express our gratitude to the anonymous referees who provided constructive
comments that helped us improve the quality of the paper.
article_number: e0253851
article_processing_charge: Yes
article_type: original
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Beata
full_name: Graff, Beata
last_name: Graff
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Dariusz
full_name: Gąsecki, Dariusz
last_name: Gąsecki
- first_name: Krzysztof
full_name: Narkiewicz, Krzysztof
last_name: Narkiewicz
citation:
ama: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent
homology as a new method of the assessment of heart rate variability. PLoS
ONE. 2021;16(7). doi:10.1371/journal.pone.0253851
apa: Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz,
K. (2021). Persistent homology as a new method of the assessment of heart rate
variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851
chicago: Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz
Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the
Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0253851.
ieee: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz,
“Persistent homology as a new method of the assessment of heart rate variability,”
PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021.
Persistent homology as a new method of the assessment of heart rate variability.
PLoS ONE. 16(7), e0253851.
mla: Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment
of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public
Library of Science, 2021, doi:10.1371/journal.pone.0253851.
short: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:21:42Z
day: '01'
ddc:
- '006'
department:
- _id: HeEd
doi: 10.1371/journal.pone.0253851
external_id:
isi:
- '000678124900050'
pmid:
- '34292957'
file:
- access_level: open_access
checksum: 0277aa155d5db1febd2cb384768bba5f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:25:41Z
date_updated: 2021-08-09T09:25:41Z
file_id: '9832'
file_name: 2021_PLoSONE_Graff.pdf
file_size: 2706919
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:25:41Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent homology as a new method of the assessment of heart rate variability
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: 16
year: '2021'
...
---
_id: '9820'
abstract:
- lang: eng
text: Material appearance hinges on material reflectance properties but also surface
geometry and illumination. The unlimited number of potential combinations between
these factors makes understanding and predicting material appearance a very challenging
task. In this work, we collect a large-scale dataset of perceptual ratings of
appearance attributes with more than 215,680 responses for 42,120 distinct combinations
of material, shape, and illumination. The goal of this dataset is twofold. First,
we analyze for the first time the effects of illumination and geometry in material
perception across such a large collection of varied appearances. We connect our
findings to those of the literature, discussing how previous knowledge generalizes
across very diverse materials, shapes, and illuminations. Second, we use the collected
dataset to train a deep learning architecture for predicting perceptual attributes
that correlate with human judgments. We demonstrate the consistent and robust
behavior of our predictor in various challenging scenarios, which, for the first
time, enables estimating perceived material attributes from general 2D images.
Since our predictor relies on the final appearance in an image, it can compare
appearance properties across different geometries and illumination conditions.
Finally, we demonstrate several applications that use our predictor, including
appearance reproduction using 3D printing, BRDF editing by integrating our predictor
in a differentiable renderer, illumination design, or material recommendations
for scene design.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement
Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement
Nº 804226 (PERDY).
article_number: '125'
article_processing_charge: No
article_type: original
author:
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
citation:
ama: 'Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on
material perception: Model and applications. ACM Transactions on Graphics.
2021;40(4). doi:10.1145/3450626.3459813'
apa: 'Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &
Myszkowski, K. (2021). The effect of shape and illumination on material perception:
Model and applications. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3450626.3459813'
chicago: 'Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel,
Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material
Perception: Model and Applications.” ACM Transactions on Graphics. Association
for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.'
ieee: 'A. Serrano et al., “The effect of shape and illumination on material
perception: Model and applications,” ACM Transactions on Graphics, vol.
40, no. 4. Association for Computing Machinery, 2021.'
ista: 'Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K.
2021. The effect of shape and illumination on material perception: Model and applications.
ACM Transactions on Graphics. 40(4), 125.'
mla: 'Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception:
Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4,
125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.'
short: A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski,
ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:20:10Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/3450626.3459813
external_id:
isi:
- '000674930900090'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://zaguan.unizar.es/record/110704/files/texto_completo.pdf
month: '08'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The effect of shape and illumination on material perception: Model and applications'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9818'
abstract:
- lang: eng
text: Triangle mesh-based simulations are able to produce satisfying animations
of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level
simulations. Naive texturing approaches do not consider yarn-level physics, while
full yarn-level simulations may become prohibitively expensive for large garments.
We propose a method to animate yarn-level cloth geometry on top of an underlying
deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate
precomputed yarn geometry, we are able to reproduce effects such as knit loops
tightening under stretching. In combination with precomputed mesh animation or
real-time mesh simulation, our method is able to animate yarn-level cloth in real-time
at large scales.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback. We also thank
Seddi Labs for providing the garment model with fold-over seams.\r\nThis research
was supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific\r\nComputing. 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. Rahul Narain is supported
by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc."
article_number: '168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- 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: Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry.
ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation
of yarn pattern geometry. ACM Transactions on Graphics. Association for
Computing Machinery. https://doi.org/10.1145/3450626.3459816
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern
geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for
Computing Machinery, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern
geometry. ACM Transactions on Graphics. 40(4), 168.
mla: Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.”
ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing
Machinery, 2021, doi:10.1145/3450626.3459816.
short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
day: '01'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3450626.3459816
ec_funded: 1
external_id:
isi:
- '000674930900132'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3450626.3459816
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/knitting-virtual-yarn/
record:
- id: '12358'
relation: dissertation_contains
status: public
- id: '9327'
relation: software
status: public
scopus_import: '1'
status: public
title: Mechanics-aware deformation of yarn pattern geometry
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...