---
_id: '6965'
abstract:
- lang: eng
text: The central object of investigation of this paper is the Hirzebruch class,
a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The
generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following
the work of Weber, we investigate its equivariant version for (possibly singular)
toric varieties. The local decomposition of the Hirzebruch class to the fixed
points of the torus action and a formula for the local class in terms of the defining
fan are recalled. After this review part, we prove the positivity of local Hirzebruch
classes for all toric varieties, thus proving false the alleged counterexample
given by Weber.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kamil P
full_name: Rychlewicz, Kamil P
id: 85A07246-A8BF-11E9-B4FA-D9E3E5697425
last_name: Rychlewicz
citation:
ama: Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric
varieties. Bulletin of the London Mathematical Society. 2021;53(2):560-574.
doi:10.1112/blms.12442
apa: Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class
for toric varieties. Bulletin of the London Mathematical Society. Wiley.
https://doi.org/10.1112/blms.12442
chicago: Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class
for Toric Varieties.” Bulletin of the London Mathematical Society. Wiley,
2021. https://doi.org/10.1112/blms.12442.
ieee: K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for
toric varieties,” Bulletin of the London Mathematical Society, vol. 53,
no. 2. Wiley, pp. 560–574, 2021.
ista: Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class
for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574.
mla: Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class
for Toric Varieties.” Bulletin of the London Mathematical Society, vol.
53, no. 2, Wiley, 2021, pp. 560–74, doi:10.1112/blms.12442.
short: K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.
corr_author: '1'
date_created: 2019-10-24T08:04:09Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2024-10-09T20:59:03Z
day: '01'
department:
- _id: TaHa
doi: 10.1112/blms.12442
external_id:
arxiv:
- '1910.10435'
isi:
- '000594805800001'
intvolume: ' 53'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.10435
month: '04'
oa: 1
oa_version: Preprint
page: 560-574
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The positivity of local equivariant Hirzebruch class for toric varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2021'
...
---
OA_place: publisher
OA_type: green
_id: '6995'
abstract:
- lang: eng
text: Human brain organoids represent a powerful tool for the study of human neurological
diseases particularly those that impact brain growth and structure. However, many
neurological diseases lack obvious anatomical abnormalities, yet significantly
impact neural network functions, raising the question of whether organoids possess
sufficient neural network architecture and complexity to model these conditions.
Here, we explore the network level functions of brain organoids using calcium
sensor imaging and extracellular recording approaches that together reveal the
existence of complex oscillatory network behaviors reminiscent of intact brain
preparations. We further demonstrate strikingly abnormal epileptiform network
activity in organoids derived from a Rett Syndrome patient despite only modest
anatomical differences from isogenically matched controls, and rescue with an
unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide
an essential foundation for the utilization of human brain organoids to study
intact and disordered human brain network formation and illustrate their utility
in therapeutic discovery.
acknowledgement: We thank S. Butler, T. Carmichael and members of the laboratory of
B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and
F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa
and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad
Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities
Research Center microscopy cores for access to imaging facilities. This work was
supported by grants from the California Institute for Regenerative Medicine (CIRM)
(DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897
and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922,
R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.;
R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards
from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program
(to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA
BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical
and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers
Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons
Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S.
and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience
Training Grant (R25NS065723), a Research and Training Fellowship from the American
Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist
training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose
Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral
training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M.
and A.K. were supported in part by the UCLA-California State University Northridge
CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of
the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics
Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the
NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative
and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and
the Quantitative and Computational Biosciences Collaboratory community, directed
by M. Pellegrini.
article_processing_charge: No
article_type: review
author:
- first_name: Ranmal A.
full_name: Samarasinghe, Ranmal A.
last_name: Samarasinghe
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
- first_name: Jessie E.
full_name: Buth, Jessie E.
last_name: Buth
- first_name: Simon
full_name: Mitchell, Simon
last_name: Mitchell
- first_name: Isabella
full_name: Ferando, Isabella
last_name: Ferando
- first_name: Momoko
full_name: Watanabe, Momoko
last_name: Watanabe
- first_name: Arinnae
full_name: Kurdian, Arinnae
last_name: Kurdian
- first_name: Peyman
full_name: Golshani, Peyman
last_name: Golshani
- first_name: Kathrin
full_name: Plath, Kathrin
last_name: Plath
- first_name: William E.
full_name: Lowry, William E.
last_name: Lowry
- first_name: Jack M.
full_name: Parent, Jack M.
last_name: Parent
- first_name: Istvan
full_name: Mody, Istvan
last_name: Mody
- first_name: Bennett G.
full_name: Novitch, Bennett G.
last_name: Novitch
citation:
ama: Samarasinghe RA, Miranda O, Buth JE, et al. Identification of neural oscillations
and epileptiform changes in human brain organoids. Nature Neuroscience.
2021;24:32. doi:10.1038/s41593-021-00906-5
apa: Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe,
M., … Novitch, B. G. (2021). Identification of neural oscillations and epileptiform
changes in human brain organoids. Nature Neuroscience. Springer Nature.
https://doi.org/10.1038/s41593-021-00906-5
chicago: Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell,
Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. “Identification of
Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” Nature
Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00906-5.
ieee: R. A. Samarasinghe et al., “Identification of neural oscillations and
epileptiform changes in human brain organoids,” Nature Neuroscience, vol.
24. Springer Nature, p. 32, 2021.
ista: Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian
A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification
of neural oscillations and epileptiform changes in human brain organoids. Nature
Neuroscience. 24, 32.
mla: Samarasinghe, Ranmal A., et al. “Identification of Neural Oscillations and
Epileptiform Changes in Human Brain Organoids.” Nature Neuroscience, vol.
24, Springer Nature, 2021, p. 32, doi:10.1038/s41593-021-00906-5.
short: R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe,
A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch,
Nature Neuroscience 24 (2021) 32.
date_created: 2019-11-10T11:23:58Z
date_published: 2021-08-23T00:00:00Z
date_updated: 2025-07-09T09:00:12Z
day: '23'
department:
- _id: GradSch
- _id: SiHi
doi: 10.1038/s41593-021-00906-5
external_id:
isi:
- '000687516300001'
pmid:
- '34426698 '
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/820183
month: '08'
oa: 1
oa_version: Preprint
page: '32'
pmid: 1
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of neural oscillations and epileptiform changes in human brain
organoids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2021'
...
---
_id: '7463'
abstract:
- lang: eng
text: Resting-state brain activity is characterized by the presence of neuronal
avalanches showing absence of characteristic size. Such evidence has been interpreted
in the context of criticality and associated with the normal functioning of the
brain. A distinctive attribute of systems at criticality is the presence of long-range
correlations. Thus, to verify the hypothesis that the brain operates close to
a critical point and consequently assess deviations from criticality for diagnostic
purposes, it is of primary importance to robustly and reliably characterize correlations
in resting-state brain activity. Recent works focused on the analysis of narrow-band
electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude
envelope, showing evidence of long-range temporal correlations (LRTC) in neural
oscillations. However, brain activity is a broadband phenomenon, and a significant
piece of information useful to precisely discriminate between normal (critical)
and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal
cortical dynamics. Here we propose to characterize the temporal correlations in
the broadband brain activity through the lens of neuronal avalanches. To this
end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding
neuronal avalanche sequences, and study their temporal correlations. We demonstrate
that the broadband resting-state brain activity consistently exhibits long-range
power-law correlations in both EEG and MEG recordings, with similar values of
the scaling exponents. Importantly, although we observe that the avalanche size
distribution depends on scale parameters, scaling exponents characterizing long-range
correlations are quite robust. In particular, they are independent of the temporal
binning (scale of analysis), indicating that our analysis captures intrinsic characteristics
of the underlying dynamics. Because neuronal avalanches constitute a fundamental
feature of neural systems with universal characteristics, the proposed approach
may serve as a general, systems- and experiment-independent procedure to infer
the existence of underlying long-range correlations in extended neural systems,
and identify pathological behaviors in the complex spatio-temporal interplay of
cortical rhythms.
acknowledgement: LdA would like to acknowledge the financial support from MIUR-PRIN2017
WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies
CAPES and FUNCAP for financial support.
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Hans J
full_name: Herrmann, Hans J
last_name: Herrmann
- first_name: Lucilla
full_name: de Arcangelis, Lucilla
last_name: de Arcangelis
citation:
ama: Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations
in the broadband resting state activity of the human brain revealed by neuronal
avalanches. Neurocomputing. 2021;461:657-666. doi:10.1016/j.neucom.2020.05.126
apa: Lombardi, F., Shriki, O., Herrmann, H. J., & de Arcangelis, L. (2021).
Long-range temporal correlations in the broadband resting state activity of the
human brain revealed by neuronal avalanches. Neurocomputing. Elsevier.
https://doi.org/10.1016/j.neucom.2020.05.126
chicago: Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis.
“Long-Range Temporal Correlations in the Broadband Resting State Activity of the
Human Brain Revealed by Neuronal Avalanches.” Neurocomputing. Elsevier,
2021. https://doi.org/10.1016/j.neucom.2020.05.126.
ieee: F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range
temporal correlations in the broadband resting state activity of the human brain
revealed by neuronal avalanches,” Neurocomputing, vol. 461. Elsevier, pp.
657–666, 2021.
ista: Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal
correlations in the broadband resting state activity of the human brain revealed
by neuronal avalanches. Neurocomputing. 461, 657–666.
mla: Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband
Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” Neurocomputing,
vol. 461, Elsevier, 2021, pp. 657–66, doi:10.1016/j.neucom.2020.05.126.
short: F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461
(2021) 657–666.
date_created: 2020-02-06T16:09:14Z
date_published: 2021-05-13T00:00:00Z
date_updated: 2025-04-14T07:44:02Z
day: '13'
department:
- _id: GaTk
doi: 10.1016/j.neucom.2020.05.126
ec_funded: 1
external_id:
isi:
- '000704086300015'
intvolume: ' 461'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.02.03.930966
month: '05'
oa: 1
oa_version: Preprint
page: 657-666
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neurocomputing
publication_identifier:
eissn:
- 1872-8286
issn:
- 0925-2312
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-range temporal correlations in the broadband resting state activity of
the human brain revealed by neuronal avalanches
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 461
year: '2021'
...
---
_id: '7551'
abstract:
- lang: eng
text: Novelty facilitates formation of memories. The detection of novelty and storage
of contextual memories are both mediated by the hippocampus, yet the mechanisms
that link these two functions remain to be defined. Dentate granule cells (GCs)
of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual
memory. However, their key excitatory inputs from the entorhinal cortex are not
responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here
we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal
mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving
dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally
regulates novelty-induced contextual memory acquisition. Our results show that
ventral MCs activity controls memory formation through an intra-hippocampal interaction
mechanism gated by novelty.
acknowledgement: We thank Peter Jonas and Peter Somogyi for critically reading the
manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the
Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also
thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L.
Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research
Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s
expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst,
and Laura Burnett for technical assistance, as well as Robert Beattie for imaging
assistance. This work was supported by a European Research Council Advanced Grant
694539 to R.S.
article_processing_charge: No
article_type: original
author:
- first_name: Felipe A
full_name: Fredes Tolorza, Felipe A
id: 384825DA-F248-11E8-B48F-1D18A9856A87
last_name: Fredes Tolorza
- first_name: Maria A
full_name: Silva Sifuentes, Maria A
id: 371B3D6E-F248-11E8-B48F-1D18A9856A87
last_name: Silva Sifuentes
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Kenta
full_name: Kobayashi, Kenta
last_name: Kobayashi
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch
MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual
memory formation. Current Biology. 2021;31(1):P25-38.E5. doi:10.1016/j.cub.2020.09.074
apa: Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi,
K., Jösch, M. A., & Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway
gates novelty-induced contextual memory formation. Current Biology. Elsevier.
https://doi.org/10.1016/j.cub.2020.09.074
chicago: Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner,
Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal
Pathway Gates Novelty-Induced Contextual Memory Formation.” Current Biology.
Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.09.074.
ieee: F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi,
M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced
contextual memory formation,” Current Biology, vol. 31, no. 1. Elsevier,
p. P25–38.E5, 2021.
ista: Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch
MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced
contextual memory formation. Current Biology. 31(1), P25–38.E5.
mla: Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates
Novelty-Induced Contextual Memory Formation.” Current Biology, vol. 31,
no. 1, Elsevier, 2021, p. P25–38.E5, doi:10.1016/j.cub.2020.09.074.
short: F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi,
M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.
date_created: 2020-02-28T10:56:18Z
date_published: 2021-01-11T00:00:00Z
date_updated: 2025-06-12T06:54:22Z
day: '11'
ddc:
- '570'
department:
- _id: MaJö
- _id: RySh
doi: 10.1016/j.cub.2020.09.074
ec_funded: 1
external_id:
isi:
- '000614361000020'
pmid:
- '33065009'
file:
- access_level: open_access
checksum: b7b9c8bc84a08befce365c675229a7d1
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T13:31:28Z
date_updated: 2020-10-19T13:31:28Z
file_id: '8678'
file_name: 2021_CurrentBiology_Fredes.pdf
file_size: 4915964
relation: main_file
success: 1
file_date_updated: 2020-10-19T13:31:28Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: P25-38.E5
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: Current Biology
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/remembering-novelty/
scopus_import: '1'
status: public
title: Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2021'
...
---
_id: '7553'
abstract:
- lang: eng
text: Normative theories and statistical inference provide complementary approaches
for the study of biological systems. A normative theory postulates that organisms
have adapted to efficiently solve essential tasks, and proceeds to mathematically
work out testable consequences of such optimality; parameters that maximize the
hypothesized organismal function can be derived ab initio, without reference to
experimental data. In contrast, statistical inference focuses on efficient utilization
of data to learn model parameters, without reference to any a priori notion of
biological function, utility, or fitness. Traditionally, these two approaches
were developed independently and applied separately. Here we unify them in a coherent
Bayesian framework that embeds a normative theory into a family of maximum-entropy
“optimization priors.” This family defines a smooth interpolation between a data-rich
inference regime (characteristic of “bottom-up” statistical models), and a data-limited
ab inito prediction regime (characteristic of “top-down” normative theory). We
demonstrate the applicability of our framework using data from the visual cortex,
and argue that the flexibility it affords is essential to address a number of
fundamental challenges relating to inference and prediction in complex, high-dimensional
biological problems.
acknowledgement: The authors thank Dario Ringach for providing the V1 receptive fields
and Olivier Marre for providing the retinal receptive fields. W.M. was funded by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers
Science grant no. HFSP RGP0032/2018.
article_processing_charge: No
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality
of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
apa: Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical
analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020
chicago: Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik.
“Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press,
2021. https://doi.org/10.1016/j.neuron.2021.01.020.
ieee: W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical
analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell
Press, p. 1227–1241.e5, 2021.
ista: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis
and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.
mla: Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural
Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
short: W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021)
1227–1241.e5.
corr_author: '1'
date_created: 2020-02-28T11:00:12Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2026-04-07T12:59:24Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.neuron.2021.01.020
ec_funded: 1
external_id:
isi:
- '000637809600006'
pmid:
- '33592180'
intvolume: ' 109'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/848374
month: '04'
oa: 1
oa_version: Preprint
page: 1227-1241.e5
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neuron
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/can-evolution-be-predicted/
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Statistical analysis and optimality of neural systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2021'
...
---
_id: '9874'
abstract:
- lang: eng
text: Myocardial regeneration is restricted to early postnatal life, when mammalian
cardiomyocytes still retain the ability to proliferate. The molecular cues that
induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
is higher expressed in the early postnatal myocardium and decreases in expression
towards adulthood, especially under conditions of overload, and orchestrates the
transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
heart provokes cardiomyocyte proliferation by targeting a network of negative
cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
remodeling to overload by derepression of the prohypertrophic transcription factors
Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
provokes nearly complete regeneration of the adult myocardium after ischemic injury.
Our data demonstrate that exploitation of conserved molecular programs can enhance
the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
(EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Raso, Andrea
last_name: Raso
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Vasco
full_name: Sampaio-Pinto, Vasco
last_name: Sampaio-Pinto
- first_name: Hamid
full_name: el Azzouzi, Hamid
last_name: el Azzouzi
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Daniel W.
full_name: Sorensen, Daniel W.
last_name: Sorensen
- first_name: Lara
full_name: Ottaviani, Lara
last_name: Ottaviani
- first_name: Servé
full_name: Olieslagers, Servé
last_name: Olieslagers
- first_name: Manon M.
full_name: Huibers, Manon M.
last_name: Huibers
- first_name: Roel
full_name: de Weger, Roel
last_name: de Weger
- first_name: Sailay
full_name: Siddiqi, Sailay
last_name: Siddiqi
- first_name: Silvia
full_name: Moimas, Silvia
last_name: Moimas
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Lorena
full_name: Zentillin, Lorena
last_name: Zentillin
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Diana S.
full_name: Nascimento, Diana S.
last_name: Nascimento
- first_name: Paula A.
full_name: da Costa Martins, Paula A.
last_name: da Costa Martins
- first_name: Jop H.
full_name: van Berlo, Jop H.
last_name: van Berlo
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
- first_name: Leon J.
full_name: De Windt, Leon J.
last_name: De Windt
citation:
ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4
apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4
chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.
ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
12, 4808.
mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications,
vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.
short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
isi:
- '000683910200042'
pmid:
- '34376683'
file:
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creator: asandaue
date_created: 2021-08-10T12:29:59Z
date_updated: 2021-08-10T12:29:59Z
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file_name: 2021_NatureCommunications_Raso.pdf
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intvolume: ' 12'
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
and hypertrophy and stimulates cardiac regeneration
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: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences of the United States of America.
2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 29. National Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences of the
United States of America. 118(29), e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2025-05-14T10:59:43Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '9891'
abstract:
- lang: eng
text: 'Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127
(2019)], we present a modified “floating crystal” trial state for jellium (also
known as the classical homogeneous electron gas) with density equal to a characteristic
function. This allows us to show that three definitions of the jellium energy
coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache
[“Equality of the Jellium and uniform electron gas next-order asymptotic terms
for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb,
and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide
in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized
energy” studied in a series of papers by Serfaty and others, and thus, by the
work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate
the jellium energy to the order n term in the logarithmic energy of n points on
the unit 2-sphere. We improve upon known lower bounds for this renormalized energy.
Additionally, we derive formulas for the jellium energy of periodic configurations.'
acknowledgement: The author would like to thank Robert Seiringer for guidance and
many helpful comments on this project. The author would also like to thank Mathieu
Lewin for his comments on the manuscript and Lorenzo Portinale for providing his
lecture notes for the course “Mathematics of quantum many-body systems” in spring
2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these
lecture notes.
article_number: '083305'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Lauritsen AB. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494
apa: Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494
chicago: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021.
https://doi.org/10.1063/5.0053494.
ieee: A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,”
Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.
ista: Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 62(8), 083305.
mla: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305,
AIP Publishing, 2021, doi:10.1063/5.0053494.
short: A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).
corr_author: '1'
date_created: 2021-08-12T07:08:36Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2024-10-09T21:00:48Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1063/5.0053494
external_id:
arxiv:
- '2103.07975'
isi:
- '000683960800003'
file:
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checksum: d035be2b894c4d50d90ac5ce252e27cd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T12:57:06Z
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relation: main_file
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file_date_updated: 2021-10-27T12:57:06Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '8'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal and periodic jellium configurations
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: 62
year: '2021'
...
---
_id: '9903'
abstract:
- lang: eng
text: Eigenstate thermalization in quantum many-body systems implies that eigenstates
at high energy are similar to random vectors. Identifying systems where at least
some eigenstates are nonthermal is an outstanding question. In this Letter we
show that interacting quantum models that have a nullspace—a degenerate subspace
of eigenstates at zero energy (zero modes), which corresponds to infinite temperature,
provide a route to nonthermal eigenstates. We analytically show the existence
of a zero mode which can be represented as a matrix product state for a certain
class of local Hamiltonians. In the more general case we use a subspace disentangling
algorithm to generate an orthogonal basis of zero modes characterized by increasing
entanglement entropy. We show evidence for an area-law entanglement scaling of
the least-entangled zero mode in the broad parameter regime, leading to a conjecture
that all local Hamiltonians with the nullspace feature zero modes with area-law
entanglement scaling and, as such, break the strong thermalization hypothesis.
Finally, we find zero modes in constrained models and propose a setup for observing
their experimental signatures.
acknowledgement: "We acknowledge useful discussions with V. Gritsev and A. Garkun
and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and
M. S. were supported by the European Research Council (ERC) under\r\nthe European
Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)"
article_number: '060602'
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
arxiv: 1
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
citation:
ama: Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces
of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602
apa: Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates
from nullspaces of local Hamiltonians. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.127.060602
chicago: Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled
Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.
ieee: V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from
nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no.
6. American Physical Society, 2021.
ista: Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from
nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.
mla: Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local
Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American
Physical Society, 2021, doi:10.1103/physrevlett.127.060602.
short: V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).
date_created: 2021-08-13T09:27:39Z
date_published: 2021-08-06T00:00:00Z
date_updated: 2026-04-07T11:48:53Z
day: '06'
ddc:
- '539'
department:
- _id: MaSe
- _id: GradSch
- _id: MiLe
doi: 10.1103/physrevlett.127.060602
ec_funded: 1
external_id:
arxiv:
- '2102.13633'
isi:
- '000684276000002'
file:
- access_level: open_access
checksum: 51218f302dcef99d90d1209809fcc874
content_type: application/pdf
creator: mserbyn
date_created: 2021-08-13T09:28:08Z
date_updated: 2021-08-13T09:28:08Z
file_id: '9904'
file_name: PhysRevLett.127.060602_SOM.pdf
file_size: 5064231
relation: main_file
success: 1
file_date_updated: 2021-08-13T09:28:08Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '19393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Area-law entangled eigenstates from nullspaces of local Hamiltonians
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: 127
year: '2021'
...
---
_id: '9906'
abstract:
- lang: eng
text: Endometriosis is a common gynecological disorder characterized by ectopic
growth of endometrium outside the uterus and is associated with chronic pain and
infertility. We investigated the role of the long intergenic noncoding RNA 01133
(LINC01133) in endometriosis, an lncRNA that has been implicated in several types
of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions.
As expression appeared higher in the epithelial endometrial layer, we performed
a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic
assays indicated that LINC01133 may promote proliferation and suppress cellular
migration, and affect the cytoskeleton and morphology of the cells. Gene ontology
analysis of differentially expressed genes indicated that cell proliferation and
migration pathways were affected in line with the observed phenotype. We validated
upregulation of p21 and downregulation of Cyclin A at the protein level, which
together with the quantification of the DNA content using fluorescence-activated
cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation
may be due to changes in cell cycle. Further, we found testis-specific protein
kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation
of actin severing protein Cofilin, which could explain changes in the cytoskeleton
and cellular migration. These results indicate that endometriosis is associated
with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation
and migration pathways.
acknowledgement: "Open access funding provided by Medical University of Vienna. The
authors would like to thank all the participants and health professionals involved
in the present study. We want to thank our technical assistants Barbara Widmar and
Matthias Witzmann-Stern for their diligent work and constant assistance. We would
like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and
resources."
article_number: '8385'
article_processing_charge: Yes
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Isabella
full_name: Haslinger, Isabella
last_name: Haslinger
- first_name: Lorenz
full_name: Kuessel, Lorenz
last_name: Kuessel
- first_name: Alexandra
full_name: Perricos, Alexandra
last_name: Perricos
- first_name: Heinrich
full_name: Husslein, Heinrich
last_name: Husslein
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
citation:
ama: Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes
proliferation in an endometriosis epithelial cell line. International Journal
of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385
apa: Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel,
L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms22168385
chicago: Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling,
Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and
René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis
Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI,
2021. https://doi.org/10.3390/ijms22168385.
ieee: I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line,” International Journal of Molecular
Sciences, vol. 22, no. 16. MDPI, 2021.
ista: Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos
A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular Sciences.
22(16), 8385.
mla: Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation
in an Endometriosis Epithelial Cell Line.” International Journal of Molecular
Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.
short: I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel,
A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2025-06-12T06:29:07Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/ijms22168385
external_id:
isi:
- '000689147400001'
pmid:
- '34445100'
file:
- access_level: open_access
checksum: be7f0042607ca60549cb27513c19c6af
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:29:17Z
date_updated: 2021-08-16T09:29:17Z
file_id: '9922'
file_name: 2021_InternationalJournalOfMolecularSciences_Yotova.pdf
file_size: 2646018
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:29:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01133 inhibits invasion and promotes proliferation in an endometriosis
epithelial cell line
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2021'
...
---
_id: '9907'
abstract:
- lang: eng
text: 'DivIVA is a protein initially identified as a spatial regulator of cell division
in the model organism Bacillus subtilis, but its homologues are present in many
other Gram-positive bacteria, including Clostridia species. Besides its role as
topological regulator of the Min system during bacterial cell division, DivIVA
is involved in chromosome segregation during sporulation, genetic competence,
and cell wall synthesis. DivIVA localizes to regions of high membrane curvature,
such as the cell poles and cell division site, where it recruits distinct binding
partners. Previously, it was suggested that negative curvature sensing is the
main mechanism by which DivIVA binds to these specific regions. Here, we show
that Clostridioides difficile DivIVA binds preferably to membranes containing
negatively charged phospholipids, especially cardiolipin. Strikingly, we observed
that upon binding, DivIVA modifies the lipid distribution and induces changes
to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA
might play a more complex and so far unknown active role during the formation
of the cell division septal membrane. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova
and other members of Barák’s laboratory for useful discussions, suggestions and
help. Special thanks also to Emília Chovancová for technical support. We are grateful
to Juraj Labaj for drawing the model and for help with graphics. Many thanks to
all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp
Radler, and other members of the Loose’s laboratory for sharing their knowledge
of SLB preparation and TIRF experiment chambers, for sharing coverslips and for
help with the TIRF microscope and data analysis. We also thank the members of the
Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and
Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J.
Bauer for critically reading the manuscript."
article_number: '8350'
article_processing_charge: Yes
article_type: original
author:
- first_name: Naďa
full_name: Labajová, Naďa
last_name: Labajová
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Miroslav
full_name: Jurásek, Miroslav
last_name: Jurásek
- first_name: Robert
full_name: Vácha, Robert
last_name: Vácha
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Imrich
full_name: Barák, Imrich
last_name: Barák
citation:
ama: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350
apa: Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák,
I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350
chicago: Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin
Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial
Cell Division Protein Diviva.” International Journal of Molecular Sciences.
MDPI, 2021. https://doi.org/10.3390/ijms22158350.
ieee: N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák,
“Cardiolipin-containing lipid membranes attract the bacterial cell division protein
diviva,” International Journal of Molecular Sciences, vol. 22, no. 15.
MDPI, 2021.
ista: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 22(15), 8350.
mla: Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the
Bacterial Cell Division Protein Diviva.” International Journal of Molecular
Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.
short: N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International
Journal of Molecular Sciences 22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2025-07-10T12:02:05Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.3390/ijms22158350
ec_funded: 1
external_id:
isi:
- '000681815400001'
pmid:
- '34361115'
file:
- access_level: open_access
checksum: a4bc06e9a2c803ceff5a91f10b174054
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:35:56Z
date_updated: 2021-08-16T09:35:56Z
file_id: '9923'
file_name: 2021_InternationalJournalOfMolecularSciences_Labajová .pdf
file_size: 6132410
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:35:56Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2021'
...
---
_id: '9908'
abstract:
- lang: eng
text: About eight million animal species are estimated to live on Earth, and all
except those belonging to one subphylum are invertebrates. Invertebrates are incredibly
diverse in their morphologies, life histories, and in the range of the ecological
niches that they occupy. A great variety of modes of reproduction and sex determination
systems is also observed among them, and their mosaic-distribution across the
phylogeny shows that transitions between them occur frequently and rapidly. Genetic
conflict in its various forms is a long-standing theory to explain what drives
those evolutionary transitions. Here, we review (1) the different modes of reproduction
among invertebrate species, highlighting sexual reproduction as the probable ancestral
state; (2) the paradoxical diversity of sex determination systems; (3) the different
types of genetic conflicts that could drive the evolution of such different systems.
article_number: '1136'
article_processing_charge: Yes
article_type: review
author:
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Stéphanie
full_name: Bertrand, Stéphanie
last_name: Bertrand
- first_name: Hector
full_name: Escriva, Hector
last_name: Escriva
citation:
ama: Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136
apa: Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity
of modes of reproduction and sex determination systems in invertebrates, and the
putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136
chicago: Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva.
“Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates,
and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021.
https://doi.org/10.3390/genes12081136.
ieee: M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes
of reproduction and sex determination systems in invertebrates, and the putative
contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 12(8), 1136.
mla: Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination
Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.”
Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.
short: M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2026-04-02T14:05:14Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes12081136
ec_funded: 1
external_id:
isi:
- '000690475900001'
pmid:
- '34440310'
file:
- access_level: open_access
checksum: 744e60e56d290a96da3c91a9779f886f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:49:35Z
date_updated: 2021-08-16T09:49:35Z
file_id: '9926'
file_name: 2021_Genes_Picard.pdf
file_size: 2297655
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:49:35Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genes
publication_identifier:
eissn:
- 2073-4425
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diversity of modes of reproduction and sex determination systems in invertebrates,
and the putative contribution of genetic conflict
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12
year: '2021'
...
---
_id: '9909'
abstract:
- lang: eng
text: Roots are composed of different root types and, in the dicotyledonous Arabidopsis,
typically consist of a primary root that branches into lateral roots. Adventitious
roots emerge from non-root tissue and are formed upon wounding or other types
of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis
hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously
applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was
less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a
more potent inhibitor at concentrations above 1 µM, suggesting that it was more
selective in triggering a root inhibition response. Analysis of a series of phosphonamide
and phosphonate pyrabactin analogs suggested that adventitious root formation
and lateral root branching are differentially regulated by ABA signaling. ABA
biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and
point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.
acknowledgement: We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis
mutants and ABA signaling mutants.
article_number: '1141'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yinwei
full_name: Zeng, Yinwei
last_name: Zeng
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Hoang Khai
full_name: Trinh, Hoang Khai
last_name: Trinh
- first_name: Thomas
full_name: Heugebaert, Thomas
last_name: Heugebaert
- first_name: Christian V.
full_name: Stevens, Christian V.
last_name: Stevens
- first_name: Irene
full_name: Garcia-Maquilon, Irene
last_name: Garcia-Maquilon
- first_name: Pedro L.
full_name: Rodriguez, Pedro L.
last_name: Rodriguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
citation:
ama: Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141
apa: Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon,
I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is
suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141
chicago: Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian
V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny
Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA
Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.
ieee: Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation
is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon
I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 12(8), 1141.
mla: Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is
Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021,
doi:10.3390/genes12081141.
short: Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon,
P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2026-04-02T13:57:06Z
day: '27'
ddc:
- '580'
- '570'
department:
- _id: JiFr
doi: 10.3390/genes12081141
external_id:
isi:
- '000690558000001'
file:
- access_level: open_access
checksum: 3d99535618cf9a5b14d264408fa52e97
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:02:40Z
date_updated: 2021-08-16T09:02:40Z
file_id: '9919'
file_name: 2021_Genes_Zeng.pdf
file_size: 1340305
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:02:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genes
publication_identifier:
eissn:
- 2073-4425
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12
year: '2021'
...
---
_id: '9910'
abstract:
- lang: eng
text: Adult height inspired the first biometrical and quantitative genetic studies
and is a test-case trait for understanding heritability. The studies of height
led to formulation of the classical polygenic model, that has a profound influence
on the way we view and analyse complex traits. An essential part of the classical
model is an assumption of additivity of effects and normality of the distribution
of the residuals. However, it may be expected that the normal approximation will
become insufficient in bigger studies. Here, we demonstrate that when the height
of hundreds of thousands of individuals is analysed, the model complexity needs
to be increased to include non-additive interactions between sex, environment
and genes. Alternatively, the use of log-normal approximation allowed us to still
use the additive effects model. These findings are important for future genetic
and methodologic studies that make use of adult height as an exemplar trait.
acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful
discussion and help with conceptualising our findings and to Lennart C. Karssen
for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has
been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects
in control of complex human traits”). The work of SAS, IAK, and TIS were supported
by Russian Ministry of Science and Education under the 5–100 Excellence Programme.
The work of YSA and TIA was supported by the Ministry of Education and Science of
the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4).
FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sergei A.
full_name: Slavskii, Sergei A.
last_name: Slavskii
- first_name: Ivan A.
full_name: Kuznetsov, Ivan A.
last_name: Kuznetsov
- first_name: Tatiana I.
full_name: Shashkova, Tatiana I.
last_name: Shashkova
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Tatiana I.
full_name: Axenovich, Tatiana I.
last_name: Axenovich
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yurii S.
full_name: Aulchenko, Yurii S.
last_name: Aulchenko
citation:
ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation
for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091.
doi:10.1038/s41431-021-00836-7
apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich,
T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation
for adult height. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-021-00836-7
chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A.
Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The
Limits of Normal Approximation for Adult Height.” European Journal of Human
Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.
ieee: S. A. Slavskii et al., “The limits of normal approximation for adult
height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature,
pp. 1082–1091, 2021.
ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov
F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European
Journal of Human Genetics. 29(7), 1082–1091.
mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.”
European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021,
pp. 1082–91, doi:10.1038/s41431-021-00836-7.
short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich,
F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2025-07-10T12:02:05Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1038/s41431-021-00836-7
ec_funded: 1
external_id:
isi:
- '000625853200001'
pmid:
- '33664501'
file:
- access_level: open_access
checksum: a676d76f91b0dbe0504c63e469129c2a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:14:36Z
date_updated: 2021-08-16T09:14:36Z
file_id: '9921'
file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf
file_size: 1079395
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:14:36Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1082-1091
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- 1476-5438
issn:
- 1018-4813
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The limits of normal approximation for adult height
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2021'
...
---
_id: '9911'
abstract:
- lang: eng
text: A modern day light microscope has evolved from a tool devoted to making primarily
empirical observations to what is now a sophisticated , quantitative device that
is an integral part of both physical and life science research. Nowadays, microscopes
are found in nearly every experimental laboratory. However, despite their prevalent
use in capturing and quantifying scientific phenomena, neither a thorough understanding
of the principles underlying quantitative imaging techniques nor appropriate knowledge
of how to calibrate, operate and maintain microscopes can be taken for granted.
This is clearly demonstrated by the well-documented and widespread difficulties
that are routinely encountered in evaluating acquired data and reproducing scientific
experiments. Indeed, studies have shown that more than 70% of researchers have
tried and failed to repeat another scientist's experiments, while more than half
have even failed to reproduce their own experiments. One factor behind the reproducibility
crisis of experiments published in scientific journals is the frequent underreporting
of imaging methods caused by a lack of awareness and/or a lack of knowledge of
the applied technique. Whereas quality control procedures for some methods used
in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry,
have been introduced (e.g. ENCODE), this issue has not been tackled for optical
microscopy instrumentation and images. Although many calibration standards and
protocols have been published, there is a lack of awareness and agreement on common
standards and guidelines for quality assessment and reproducibility. In April
2020, the QUality Assessment and REProducibility for instruments and images in
Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises
imaging scientists from academia and industry who share a common interest in achieving
a better understanding of the performance and limitations of microscopes and improved
quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi
initiative is to establish a set of common QC standards, guidelines, metadata
models and tools, including detailed protocols, with the ultimate aim of improving
reproducible advances in scientific research. This White Paper (1) summarizes
the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi
initiative; (2) identifies the urgent need to address these obstacles in a grassroots
manner, through a community of stakeholders including, researchers, imaging scientists,
bioimage analysts, bioimage informatics developers, corporate partners, funding
agencies, standards organizations, scientific publishers and observers of such;
(3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes
future steps that can be taken to improve the dissemination and acceptance of
the proposed guidelines to manage QC. To summarize, the principal goal of the
QUAREP-LiMi initiative is to improve the overall quality and reproducibility of
light microscope image data by introducing broadly accepted standard practices
and accurately captured image data metrics.
acknowledgement: We thank https://www.somersault1824.com/somersault18:24 BV (Leuven,
Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122,
in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap
of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.
article_processing_charge: Yes
article_type: original
author:
- first_name: Glyn
full_name: Nelson, Glyn
last_name: Nelson
- first_name: Ulrike
full_name: Boehm, Ulrike
last_name: Boehm
- first_name: Steve
full_name: Bagley, Steve
last_name: Bagley
- first_name: Peter
full_name: Bajcsy, Peter
last_name: Bajcsy
- first_name: Johanna
full_name: Bischof, Johanna
last_name: Bischof
- first_name: Claire M.
full_name: Brown, Claire M.
last_name: Brown
- first_name: Aurélien
full_name: Dauphin, Aurélien
last_name: Dauphin
- first_name: Ian M.
full_name: Dobbie, Ian M.
last_name: Dobbie
- first_name: John E.
full_name: Eriksson, John E.
last_name: Eriksson
- first_name: Orestis
full_name: Faklaris, Orestis
last_name: Faklaris
- first_name: Julia
full_name: Fernandez-Rodriguez, Julia
last_name: Fernandez-Rodriguez
- first_name: Alexia
full_name: Ferrand, Alexia
last_name: Ferrand
- first_name: Laurent
full_name: Gelman, Laurent
last_name: Gelman
- first_name: Ali
full_name: Gheisari, Ali
last_name: Gheisari
- first_name: Hella
full_name: Hartmann, Hella
last_name: Hartmann
- first_name: Christian
full_name: Kukat, Christian
last_name: Kukat
- first_name: Alex
full_name: Laude, Alex
last_name: Laude
- first_name: Miso
full_name: Mitkovski, Miso
last_name: Mitkovski
- first_name: Sebastian
full_name: Munck, Sebastian
last_name: Munck
- first_name: Alison J.
full_name: North, Alison J.
last_name: North
- first_name: Tobias M.
full_name: Rasse, Tobias M.
last_name: Rasse
- first_name: Ute
full_name: Resch-Genger, Ute
last_name: Resch-Genger
- first_name: Lucas C.
full_name: Schuetz, Lucas C.
last_name: Schuetz
- first_name: Arne
full_name: Seitz, Arne
last_name: Seitz
- first_name: Caterina
full_name: Strambio-De-Castillia, Caterina
last_name: Strambio-De-Castillia
- first_name: Jason R.
full_name: Swedlow, Jason R.
last_name: Swedlow
- first_name: Ioannis
full_name: Alexopoulos, Ioannis
last_name: Alexopoulos
- first_name: Karin
full_name: Aumayr, Karin
last_name: Aumayr
- first_name: Sergiy
full_name: Avilov, Sergiy
last_name: Avilov
- first_name: Gert Jan
full_name: Bakker, Gert Jan
last_name: Bakker
- first_name: Rodrigo R.
full_name: Bammann, Rodrigo R.
last_name: Bammann
- first_name: Andrea
full_name: Bassi, Andrea
last_name: Bassi
- first_name: Hannes
full_name: Beckert, Hannes
last_name: Beckert
- first_name: Sebastian
full_name: Beer, Sebastian
last_name: Beer
- first_name: Yury
full_name: Belyaev, Yury
last_name: Belyaev
- first_name: Jakob
full_name: Bierwagen, Jakob
last_name: Bierwagen
- first_name: Konstantin A.
full_name: Birngruber, Konstantin A.
last_name: Birngruber
- first_name: Manel
full_name: Bosch, Manel
last_name: Bosch
- first_name: Juergen
full_name: Breitlow, Juergen
last_name: Breitlow
- first_name: Lisa A.
full_name: Cameron, Lisa A.
last_name: Cameron
- first_name: Joe
full_name: Chalfoun, Joe
last_name: Chalfoun
- first_name: James J.
full_name: Chambers, James J.
last_name: Chambers
- first_name: Chieh Li
full_name: Chen, Chieh Li
last_name: Chen
- first_name: Eduardo
full_name: Conde-Sousa, Eduardo
last_name: Conde-Sousa
- first_name: Alexander D.
full_name: Corbett, Alexander D.
last_name: Corbett
- first_name: Fabrice P.
full_name: Cordelieres, Fabrice P.
last_name: Cordelieres
- first_name: Elaine Del
full_name: Nery, Elaine Del
last_name: Nery
- first_name: Ralf
full_name: Dietzel, Ralf
last_name: Dietzel
- first_name: Frank
full_name: Eismann, Frank
last_name: Eismann
- first_name: Elnaz
full_name: Fazeli, Elnaz
last_name: Fazeli
- first_name: Andreas
full_name: Felscher, Andreas
last_name: Felscher
- first_name: Hans
full_name: Fried, Hans
last_name: Fried
- first_name: Nathalie
full_name: Gaudreault, Nathalie
last_name: Gaudreault
- first_name: Wah Ing
full_name: Goh, Wah Ing
last_name: Goh
- first_name: Thomas
full_name: Guilbert, Thomas
last_name: Guilbert
- first_name: Roland
full_name: Hadleigh, Roland
last_name: Hadleigh
- first_name: Peter
full_name: Hemmerich, Peter
last_name: Hemmerich
- first_name: Gerhard A.
full_name: Holst, Gerhard A.
last_name: Holst
- first_name: Michelle S.
full_name: Itano, Michelle S.
last_name: Itano
- first_name: Claudia B.
full_name: Jaffe, Claudia B.
last_name: Jaffe
- first_name: Helena K.
full_name: Jambor, Helena K.
last_name: Jambor
- first_name: Stuart C.
full_name: Jarvis, Stuart C.
last_name: Jarvis
- first_name: Antje
full_name: Keppler, Antje
last_name: Keppler
- first_name: David
full_name: Kirchenbuechler, David
last_name: Kirchenbuechler
- first_name: Marcel
full_name: Kirchner, Marcel
last_name: Kirchner
- first_name: Norio
full_name: Kobayashi, Norio
last_name: Kobayashi
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Susanne
full_name: Kunis, Susanne
last_name: Kunis
- first_name: Judith
full_name: Lacoste, Judith
last_name: Lacoste
- first_name: Marco
full_name: Marcello, Marco
last_name: Marcello
- first_name: Gabriel G.
full_name: Martins, Gabriel G.
last_name: Martins
- first_name: Daniel J.
full_name: Metcalf, Daniel J.
last_name: Metcalf
- first_name: Claire A.
full_name: Mitchell, Claire A.
last_name: Mitchell
- first_name: Joshua
full_name: Moore, Joshua
last_name: Moore
- first_name: Tobias
full_name: Mueller, Tobias
last_name: Mueller
- first_name: Michael S.
full_name: Nelson, Michael S.
last_name: Nelson
- first_name: Stephen
full_name: Ogg, Stephen
last_name: Ogg
- first_name: Shuichi
full_name: Onami, Shuichi
last_name: Onami
- first_name: Alexandra L.
full_name: Palmer, Alexandra L.
last_name: Palmer
- first_name: Perrine
full_name: Paul-Gilloteaux, Perrine
last_name: Paul-Gilloteaux
- first_name: Jaime A.
full_name: Pimentel, Jaime A.
last_name: Pimentel
- first_name: Laure
full_name: Plantard, Laure
last_name: Plantard
- first_name: Santosh
full_name: Podder, Santosh
last_name: Podder
- first_name: Elton
full_name: Rexhepaj, Elton
last_name: Rexhepaj
- first_name: Arnaud
full_name: Royon, Arnaud
last_name: Royon
- first_name: Markku A.
full_name: Saari, Markku A.
last_name: Saari
- first_name: Damien
full_name: Schapman, Damien
last_name: Schapman
- first_name: Vincent
full_name: Schoonderwoert, Vincent
last_name: Schoonderwoert
- first_name: Britta
full_name: Schroth-Diez, Britta
last_name: Schroth-Diez
- first_name: Stanley
full_name: Schwartz, Stanley
last_name: Schwartz
- first_name: Michael
full_name: Shaw, Michael
last_name: Shaw
- first_name: Martin
full_name: Spitaler, Martin
last_name: Spitaler
- first_name: Martin T.
full_name: Stoeckl, Martin T.
last_name: Stoeckl
- first_name: Damir
full_name: Sudar, Damir
last_name: Sudar
- first_name: Jeremie
full_name: Teillon, Jeremie
last_name: Teillon
- first_name: Stefan
full_name: Terjung, Stefan
last_name: Terjung
- first_name: Roland
full_name: Thuenauer, Roland
last_name: Thuenauer
- first_name: Christian D.
full_name: Wilms, Christian D.
last_name: Wilms
- first_name: Graham D.
full_name: Wright, Graham D.
last_name: Wright
- first_name: Roland
full_name: Nitschke, Roland
last_name: Nitschke
citation:
ama: 'Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative
to establish guidelines for quality assessment and reproducibility for instruments
and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73.
doi:10.1111/jmi.13041'
apa: 'Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M.,
… Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041'
chicago: 'Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof,
Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative
to Establish Guidelines for Quality Assessment and Reproducibility for Instruments
and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.'
ieee: 'G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp.
56–73, 2021.'
ista: 'Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. 284(1), 56–73.'
mla: 'Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish
Guidelines for Quality Assessment and Reproducibility for Instruments and Images
in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021,
pp. 56–73, doi:10.1111/jmi.13041.'
short: G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin,
I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L.
Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck,
A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia,
J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann,
A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch,
J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa,
A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli,
A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich,
G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler,
M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins,
D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami,
A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj,
A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz,
M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer,
C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-08-11T00:00:00Z
date_updated: 2026-06-18T19:59:18Z
day: '11'
ddc:
- '600'
department:
- _id: Bio
doi: 10.1111/jmi.13041
external_id:
isi:
- '000683702700001'
pmid:
- '34214188'
intvolume: ' 284'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jmi.13041
month: '08'
oa: 1
oa_version: Published Version
page: 56-73
pmid: 1
publication: Journal of Microscopy
publication_identifier:
eissn:
- 1365-2818
issn:
- 0022-2720
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'QUAREP-LiMi: A community-driven initiative to establish guidelines for quality
assessment and reproducibility for instruments and images in light microscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 284
year: '2021'
...
---
_id: '9912'
abstract:
- lang: eng
text: "In the customary random matrix model for transport in quantum dots with M
internal degrees of freedom coupled to a chaotic environment via \U0001D441≪\U0001D440
channels, the density \U0001D70C of transmission eigenvalues is computed from
a specific invariant ensemble for which explicit formula for the joint probability
density of all eigenvalues is available. We revisit this problem in the large
N regime allowing for (i) arbitrary ratio \U0001D719:=\U0001D441/\U0001D440≤1;
and (ii) general distributions for the matrix elements of the Hamiltonian of the
quantum dot. In the limit \U0001D719→0, we recover the formula for the density
\U0001D70C that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special
matrix ensemble. We also prove that the inverse square root singularity of the
density at zero and full transmission in Beenakker’s formula persists for any
\U0001D719<1 but in the borderline case \U0001D719=1 an anomalous \U0001D706−2/3
singularity arises at zero. To access this level of generality, we develop the
theory of global and local laws on the spectral density of a large class of noncommutative
rational expressions in large random matrices with i.i.d. entries."
acknowledgement: The authors are very grateful to Yan Fyodorov for discussions on
the physical background and for providing references, and to the anonymous referee
for numerous valuable remarks.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6
apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots
via noncommutative rational functions. Annales Henri Poincaré . Springer
Nature. https://doi.org/10.1007/s00023-021-01085-6
chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum
Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer
Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.
ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative
rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature,
pp. 4205–4269, 2021.
ista: Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 22, 4205–4269.
mla: Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational
Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp.
4205–4269, doi:10.1007/s00023-021-01085-6.
short: L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2025-04-15T08:04:59Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00023-021-01085-6
ec_funded: 1
external_id:
arxiv:
- '1911.05112'
isi:
- '000681531500001'
file:
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checksum: 8d6bac0e2b0a28539608b0538a8e3b38
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creator: dernst
date_created: 2022-05-12T12:50:27Z
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file_id: '11365'
file_name: 2021_AnnHenriPoincare_Erdoes.pdf
file_size: 1162454
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success: 1
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language:
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month: '12'
oa: 1
oa_version: Published Version
page: 4205–4269
project:
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call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: 'Annales Henri Poincaré '
publication_identifier:
eissn:
- 1424-0661
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scattering in quantum dots via noncommutative rational functions
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: 22
year: '2021'
...
---
OA_place: publisher
_id: '9920'
abstract:
- lang: eng
text: 'This work is concerned with two fascinating circuit quantum electrodynamics
components, the Josephson junction and the geometric superinductor, and the interesting
experiments that can be done by combining the two. The Josephson junction has
revolutionized the field of superconducting circuits as a non-linear dissipation-less
circuit element and is used in almost all superconducting qubit implementations
since the 90s. On the other hand, the superinductor is a relatively new circuit
element introduced as a key component of the fluxonium qubit in 2009. This is
an inductor with characteristic impedance larger than the resistance quantum and
self-resonance frequency in the GHz regime. The combination of these two elements
can occur in two fundamental ways: in parallel and in series. When connected in
parallel the two create the fluxonium qubit, a loop with large inductance and
a rich energy spectrum reliant on quantum tunneling. On the other hand placing
the two elements in series aids with the measurement of the IV curve of a single
Josephson junction in a high impedance environment. In this limit theory predicts
that the junction will behave as its dual element: the phase-slip junction. While
the Josephson junction acts as a non-linear inductor the phase-slip junction has
the behavior of a non-linear capacitance and can be used to measure new Josephson
junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch
oscillations. The latter experiment allows for a direct link between frequency
and current which is an elusive connection in quantum metrology. This work introduces
the geometric superinductor, a superconducting circuit element where the high
inductance is due to the geometry rather than the material properties of the superconductor,
realized from a highly miniaturized superconducting planar coil. These structures
will be described and characterized as resonators and qubit inductors and progress
towards the measurement of phase-locked Bloch oscillations will be presented.'
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
citation:
ama: Peruzzo M. Geometric superinductors and their applications in circuit quantum
electrodynamics. 2021. doi:10.15479/at:ista:9920
apa: Peruzzo, M. (2021). Geometric superinductors and their applications in circuit
quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920
chicago: Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit
Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920.
ieee: M. Peruzzo, “Geometric superinductors and their applications in circuit quantum
electrodynamics,” Institute of Science and Technology Austria, 2021.
ista: Peruzzo M. 2021. Geometric superinductors and their applications in circuit
quantum electrodynamics. Institute of Science and Technology Austria.
mla: Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit
Quantum Electrodynamics. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:9920.
short: M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum
Electrodynamics, Institute of Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-08-16T09:44:09Z
date_published: 2021-08-19T00:00:00Z
date_updated: 2026-04-15T06:43:02Z
day: '19'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:9920
file:
- access_level: closed
checksum: 3cd1986efde5121d7581f6fcf9090da8
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creator: mperuzzo
date_created: 2021-08-16T09:33:21Z
date_updated: 2021-09-06T08:39:47Z
file_id: '9924'
file_name: GeometricSuperinductorsForCQED.zip
file_size: 151387283
relation: source_file
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content_type: application/pdf
creator: mperuzzo
date_created: 2021-08-18T14:20:06Z
date_updated: 2021-09-06T08:39:47Z
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file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf
file_size: 17596344
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content_type: application/pdf
creator: mperuzzo
date_created: 2021-08-18T14:20:09Z
date_updated: 2021-09-06T08:39:47Z
description: Extra copy of the thesis as PDF/A-2b
file_id: '9940'
file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf
file_size: 17592425
relation: other
file_date_updated: 2021-09-06T08:39:47Z
has_accepted_license: '1'
keyword:
- quantum computing
- superinductor
- quantum metrology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '149'
publication_identifier:
isbn:
- 978-3-99078-013-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9928'
relation: part_of_dissertation
status: public
- id: '8755'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Geometric superinductors and their applications in circuit quantum electrodynamics
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '9928'
abstract:
- lang: eng
text: There are two elementary superconducting qubit types that derive directly
from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear
Josephson junction to realize the widely used charge qubits with a compact phase
variable and a discrete charge wave function. In the other, the junction is added
in parallel, which gives rise to an extended phase variable, continuous wave functions,
and a rich energy-level structure due to the loop topology. While the corresponding
rf superconducting quantum interference device Hamiltonian was introduced as a
quadratic quasi-one-dimensional potential approximation to describe the fluxonium
qubit implemented with long Josephson-junction arrays, in this work we implement
it directly using a linear superinductor formed by a single uninterrupted aluminum
wire. We present a large variety of qubits, all stemming from the same circuit
but with drastically different characteristic energy scales. This includes flux
and fluxonium qubits but also the recently introduced quasicharge qubit with strongly
enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion.
The use of a geometric inductor results in high reproducibility of the inductive
energy as guaranteed by top-down lithography—a key ingredient for intrinsically
protected superconducting qubits.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: We thank W. Hughes for analytic and numerical modeling during the
early stages of this work, J. Koch for discussions and support with the scqubits
package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros
for equipment support, as well as the MIBA workshop and the Institute of Science
and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise,
and E. Flurin for discussions. This work was supported by a NOMIS Foundation research
grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria.
M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient
of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Gregory
full_name: Szep, Gregory
last_name: Szep
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction. PRX Quantum. 2021;2(4):040341.
doi:10.1103/PRXQuantum.2.040341'
apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M.,
& Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase
delocalization across a single Josephson junction. PRX Quantum. American
Physical Society. https://doi.org/10.1103/PRXQuantum.2.040341'
chicago: 'Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko,
Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction.” PRX Quantum.
American Physical Society, 2021. https://doi.org/10.1103/PRXQuantum.2.040341.'
ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction,” PRX Quantum,
vol. 2, no. 4. American Physical Society, p. 040341, 2021.'
ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM.
2021. Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction. PRX Quantum. 2(4), 040341.'
mla: 'Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase
Delocalization across a Single Josephson Junction.” PRX Quantum, vol. 2,
no. 4, American Physical Society, 2021, p. 040341, doi:10.1103/PRXQuantum.2.040341.'
short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M.
Fink, PRX Quantum 2 (2021) 040341.
corr_author: '1'
date_created: 2021-08-17T08:14:18Z
date_published: 2021-11-24T00:00:00Z
date_updated: 2026-04-15T06:41:46Z
day: '24'
ddc:
- '530'
department:
- _id: JoFi
- _id: NanoFab
- _id: M-Shop
doi: 10.1103/PRXQuantum.2.040341
ec_funded: 1
external_id:
arxiv:
- '2106.05882'
isi:
- '000723015100001'
file:
- access_level: open_access
checksum: 36eb41ea43d8ca22b0efab12419e4eb2
content_type: application/pdf
creator: cchlebak
date_created: 2022-01-18T11:29:33Z
date_updated: 2022-01-18T11:29:33Z
file_id: '10641'
file_name: 2021_PRXQuantum_Peruzzo.pdf
file_size: 4247422
relation: main_file
success: 1
file_date_updated: 2022-01-18T11:29:33Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '4'
keyword:
- quantum physics
- mesoscale and nanoscale physics
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '040341'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2622978C-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
- id: '9920'
relation: dissertation_contains
status: public
- id: '17133'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '9933'
abstract:
- lang: eng
text: "In this paper, we study the power and limitations of component-stable algorithms
in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari,
Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space
MPC algorithms, which are, informally, defined as algorithms for which the outputs
reported by the nodes in different connected components are required to be independent.
This very natural notion was introduced to capture most (if not all) of the known
efficient MPC algorithms to date, and it was the first general class of MPC algorithms
for which one can show non-trivial conditional lower bounds. In this paper we
enhance the framework of component-stable algorithms and investigate its effect
on the complexity of randomized and deterministic low-space MPC. Our key contributions
include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and
Uitto. This requires a very delicate amendment of the notion of component stability,
which allows us to fill in gaps in the earlier arguments. 2) We also extend the
framework to obtain conditional lower bounds for deterministic algorithms and
fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate
a collection of natural graph problems for which non-component-stable algorithms
break the conditional lower bound obtained for component-stable algorithms. This
implies that, for both deterministic and randomized algorithms, component-stable
algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether
our results imply that component-stability might limit the computational power
of the low-space MPC model, paving the way for improved upper bounds that escape
the conditional lower bound setting of Ghaffari, Kuhn, and Uitto."
acknowledgement: This work is partially supported by a Weizmann-UK Making Connections
Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty
Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083,
the Minerva foundation with funding from the Federal German Ministry for Education
and Research No. 713238, and the European Union’s Horizon 2020 programme under the
Marie Skłodowska-Curie grant agreement No 754411.
article_processing_charge: No
arxiv: 1
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
citation:
ama: 'Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel
computation. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing. Association for Computing Machinery; 2021:481–491. doi:10.1145/3465084.3467903'
apa: 'Czumaj, A., Davies, P., & Parter, M. (2021). Component stability in low-space
massively parallel computation. In Proceedings of the 2021 ACM Symposium on
Principles of Distributed Computing (pp. 481–491). Virtual, Italy: Association
for Computing Machinery. https://doi.org/10.1145/3465084.3467903'
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in
Low-Space Massively Parallel Computation.” In Proceedings of the 2021 ACM Symposium
on Principles of Distributed Computing, 481–491. Association for Computing
Machinery, 2021. https://doi.org/10.1145/3465084.3467903.
ieee: A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively
parallel computation,” in Proceedings of the 2021 ACM Symposium on Principles
of Distributed Computing, Virtual, Italy, 2021, pp. 481–491.
ista: 'Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively
parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing. PODC: Principles of Distributed Computing, 481–491.'
mla: Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel
Computation.” Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing, Association for Computing Machinery, 2021, pp. 481–491, doi:10.1145/3465084.3467903.
short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery, 2021,
pp. 481–491.
conference:
end_date: 2021-07-30
location: Virtual, Italy
name: 'PODC: Principles of Distributed Computing'
start_date: 2021-07-26
date_created: 2021-08-17T18:11:16Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2025-04-14T07:43:49Z
day: '21'
department:
- _id: DaAl
doi: 10.1145/3465084.3467903
ec_funded: 1
external_id:
arxiv:
- '2106.01880'
isi:
- '000744439800049'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2106.01880
month: '07'
oa: 1
oa_version: Submitted Version
page: 481–491
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450385480'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Component stability in low-space massively parallel computation
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9935'
abstract:
- lang: eng
text: "We present a deterministic O(log log log n)-round low-space Massively Parallel
Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex
graphs. In this model, every machine has sublinear local space of size n^φ for
any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting
where each machine is allowed to perform exponential local computations, while
respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution
is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by
Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm
runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized
round complexity for the problem in the local model. Our derandomization employs
a combination of tools, notably pseudorandom generators (PRG) and bounded-independence
hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds
matches the bound of log(T_local ), which currently serves an upper bound barrier
for all known randomized algorithms for locally-checkable problems in this model.
Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the
(Δ+1)-coloring problem have been known before."
acknowledgement: This work is partially supported by a Weizmann-UK Making Connections
Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty
Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083,
the Minerva foundation with funding from the Federal German Ministry for Education
and Research No. 713238, and the European Union’s Horizon 2020 programme under the
Marie Skłodowska-Curie grant agreement No 754411.
article_processing_charge: No
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
citation:
ama: 'Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space
MPC. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing. Association for Computing Machinery; 2021:469–479. doi:10.1145/3465084.3467937'
apa: 'Czumaj, A., Davies, P., & Parter, M. (2021). Improved deterministic (Δ+1)
coloring in low-space MPC. In Proceedings of the 2021 ACM Symposium on Principles
of Distributed Computing (pp. 469–479). Virtual, Italy: Association for Computing
Machinery. https://doi.org/10.1145/3465084.3467937'
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic
(Δ+1) Coloring in Low-Space MPC.” In Proceedings of the 2021 ACM Symposium
on Principles of Distributed Computing, 469–479. Association for Computing
Machinery, 2021. https://doi.org/10.1145/3465084.3467937.
ieee: A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring
in low-space MPC,” in Proceedings of the 2021 ACM Symposium on Principles of
Distributed Computing, Virtual, Italy, 2021, pp. 469–479.
ista: 'Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring
in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed
Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.'
mla: Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.”
Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing,
Association for Computing Machinery, 2021, pp. 469–479, doi:10.1145/3465084.3467937.
short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery, 2021,
pp. 469–479.
conference:
end_date: 2021-07-30
location: Virtual, Italy
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2021-07-26
date_created: 2021-08-17T18:14:15Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2025-04-14T07:43:49Z
day: '21'
department:
- _id: DaAl
doi: 10.1145/3465084.3467937
ec_funded: 1
external_id:
isi:
- '000744439800048'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://wrap.warwick.ac.uk/153753
month: '07'
oa: 1
oa_version: Submitted Version
page: 469–479
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- 978-1-4503-8548-0
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved deterministic (Δ+1) coloring in low-space MPC
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...